1 Supplementary text and tables for

2 A frameshift is repaired through nonsense-mediated

3 gene revising in E. coli 4 Xiaolong Wang1*, Xuxiang Wang1, Chunyan Li1, Haibo Peng1, Gang Chen1, Jianye Zhang1 5 College of Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China 6

7 1. Materials and Methods in details

8 1.1 Frameshift preparation and revertant screening 9 The G:C base pair located at +136 was deleted from the wild-type bla gene (bla+) by 10 an overlapping extension chain reaction (OE-PCR). E. coli DH5α competent 11 cells were transformed with pBR322-(bla-), propagated in tetracycline broth. Dilutions 12 were plated in parallel on tetracycline plates and ampicillin plates to screen for revertants. 13 The recovery rates were calculated by a standard method [1]. The revertants were 14 propagated in ampicillin broth at 37°C with 200 rpm shaking and overnight seed culture 15 (1:50). The growth rates of the revertants were evaluated by the doubling time in their 16 exponential growth phase. Their plasmid DNA was extracted, and their bla genes were 17 sequenced by the Sanger method. 18 1.2 Construction and expression of a PTC-free frameshift 19 Usually, a suppressor tRNA gene is introduced into cells to readthrough a nonsense 20 mutation and incorporate an amino acid instead of terminating the translation. However, 21 suppressor tRNA genes are not suitable for reading through the PTCs of bla- for two 22 reasons: first, all three different PTCs (UGA, UAG, UAA) are present in bla-, we must 23 introduce three different suppressor tRNA genes. However, there is no means to restrict 24 their function to bla and not to other genes. If three suppressor tRNAs were introduced, all 25 the true termination codons of other genes would also be readthrough, producing all sorts 26 of odd peptides in the host; second, even if three different suppressor tRNAs were 27 introduced, there is no guarantee that bla- would be expressed as expected, because the

* To whom correspondence should be addressed: Xiaolong Wang, Department of Biotechnology, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, Shandong, P. R. China, Tel: 0086-139-6969-3150, E-mail: [email protected]. .

1 nonsense mRNAs may be subject to nonsense-mediated mRNA decay or translational 2 frameshifting pathways. 3 A PTC-free frameshift bla, denoted as bla#, was derived from bla- by replacing each 4 nonsense codon with a sense codon according to the readthrough rules (Table 1). A stop 5 codon, TAA, was added in the 3'-end. The bla# gene was chemically synthesized by Sangon 6 Biotech, Co. Ltd (Shanghai), inserted into the expression vector pET28a and transformed 7 into E. coli competent cells strain BL21. Since pET28a has a kanamycin resistance gene, 8 the transformants were then plated on a kanamycin plate, propagated in kanamycin broth, 9 and plated on ampicillin plates to screen for revertants. The expression of the bla# gene 10 was induced by 0.1 mM IPTG. Their total protein samples were extracted, the product was 11 purified by the nickel column chromatography and analyzed by sodium dodecyl sulfate- 12 polyacrylamide gel electrophoresis (SDS-PAGE). The purified product was tested by an 13 iodometry assay to measure its lactamase activity . 14 1.3 Plasmid and genomic DNA extraction 15 The revertant (DH5α/pBR322/bla*) was transferred in ampicillin and tetracycline 16 containing LB, and the frameshift (DH5α/pBR322/bla-) was inoculated in tetracycline 17 containing LB. After inoculation, the cells were cultured at 37 ℃ and 200 rpm for 12 h. 18 For each strain, 1.0 mL cultures were sent to Sangon Biotech Co., Ltd (Shanghai) to Sanger 19 sequence the bla and tet genes. The sequencing primer was tet-f: TAA CGC AGT CAG 20 GCA CCG t (65-83 base on plasmid pBR322). The genome DNA of the above strains were 21 extracted using genome DNA extraction kit (Tiangen). 22 1.4 Genome resequencing and structure/variation analysis 23 Library preparation and genome sequencing were conducted by a commercial service 24 provided by Novogene Co. Ltd. Paired-end reads were obtained on an Illumina HiSeq 25 250PE platform. The raw reads were trimmed by Trimmomatic (v0.39) to remove adapters 26 and low-quality sequences for each sample. The clean reads were mapped onto the 27 reference genome of E. coli K12 MG1655 (NC_000913.3) and the reference sequence of 28 plasmid pBR322 by bwa (v0.7.17); the output alignments were indexed by Samtools 29 (v0.1.18) [2], sorted by Picard (v2.23.4); then the reads around indels were realigned, and 30 single nucleotide polymorphisms (SNPs) and indels were called by GATK (v4.1.2.0) [3]. 31 Structural variations (SVs) were scanned by BreakDancer (v1.3.6) [4, 5].

1 1.5 RNA extraction 2 The wild type (DH5α/pBR322/bla+) and the revertants (DH5α/pBR322/bla*) were 3 inoculated in amp and tet containing LB, and the frameshift (DH5α/pBR322/bla-) was 4 inoculated in tet containing LB. After inoculation, the cells were cultured at 37 ℃ and 200 5 rpm for 12 h. The wild type, the frameshift and the revertants were inoculated in fresh LB 6 with appropriate antibiotics at the ratio of 1:100 and cultured at 37 ℃ and 200 rpm for 3 h 7 to log phase. The total RNA samples of the above strains were extracted using RNA 8 extraction kit (Tiangen). 9 1.6 Transcriptome analysis 10 Library preparation and RNA sequencing were conducted by a commercial service 11 (Novogene Co. Ltd). The high-quality clean reads for each sample were mapped using bwa 12 (v0.7.17) onto the reference sequence of the E. coli K12 MG1655 genome (NC_000913.3), 13 and the plasmid pBR322 (J01749.1) using Circos (v0.69) [6], the coverage depths of the 14 transcriptomic reads were displayed on a ring diagram next to those of the corresponding 15 genomic reads. 16 The expression level for each gene was calculated and analyzed as followed: 17 (1) Quantification of gene expression level 18 Bowtie (v2-2.2.3) was used for aligning the clean reads to the reference genome [7]. 19 HTSeq (v0.6.1) was used to count the numbers of reads mapped to each gene [8]. The 20 expected number of Fragments PerKilobase of transcript sequence per million base pairs 21 sequenced (FPKM) was calculated for each gene. 22 (2) Identification of differential expression genes 23 To identify differential expression genes (DEGs), read counts were adjusted by the 24 edgeR program for each genotype [9]. Differential expressions of the read counts of two 25 conditions were performed using the DEGSeq R package (1.20.0) [10]. The P values were 26 adjusted by the Benjamini & Hochberg method. The significantly differential expression 27 threshold was set as corrected P-value (q-value) < 0.005; fold change ≥ 2.0 and ≥ 1.5 are 28 considered great and moderate changes. 29 (3) GO and KEGG enrichment of the DEGs 30 Gene Ontology (GO) enrichment of the DEGs was implemented by the GOseq R 31 package [11], in which the potential gene length bias was corrected, and GO terms with

1 corrected P-value < 0.05 were considered significantly enriched by DEGs. KOBAS 2.0 [12] 2 was used to test the statistical enrichment of DEGs in the Kyoto encyclopedia of genes and 3 genomes (KEGG) pathways (http://www.genome.jp/kegg/). 4 1.7 Quantitative analysis of global proteome 5 Quantitative analysis of global proteome was performed by PTM-Biolabs (Hangzhou), 6 Co., Ltd. Peptides were loaded onto a reverse-phase pre-column (Acclaim PepMap 100), 7 separated on a reverse-phase analytical column and analyzed by Q Exactive™ hybrid 8 quadrupole-Orbitrap mass spectrometer (ThermoFisher Scientific). 9 The MS/MS data were processed using the Mascot search engine (v.2.3.0). The tandem 10 mass spectra were searched against the Uniprot database. GO annotation proteome was 11 derived from the UniProt-GOA database (http://www.ebi.ac.uk/GOA/). Identified protein 12 IDs were converted into UniProt ID and mapped to GO IDs. For the proteins unannotated 13 in the UniProt-GOA database, InterProScan is used to determine their GO annotations.

14 2. A review of previous studies that are supportive of the NMGR model

15 In the main text, the proposed NMGR model suggests that frame repair is triggered by 16 PTCs, based on RNA-directed DNA repair, and nonsense mRNAs are edited before 17 directing the repair of the coding DNA. NMGR integrates several key links, which have 18 already been intensively studied, including mRNA surveillance, mRNA processing, mRNA 19 editing, DNA recombination and repair. Like the connected pathways, frame repair should 20 be widely existing and highly conserved among species. NMGR shows consistency with 21 many previous studies. This supplementary text reviewed previous studies covering a wide 22 range of prokaryotic and eukaryotic species to gain deeper knowledge. 23 2.1 mRNA decay is linked to other nonsense mRNA processing pathways 24 In eukaryotes, NMD uses the presence of an exon junction complex (EJC) downstream 25 PTCs as a second signal to distinguish a PTC from a true stop codon [13]. In addition to 26 NMD, the nonsense mRNAs may also be subject to some other pathways, including 27 translational repression, transcriptional silencing, and alternative splicing, all of which are 28 linked to NMD [14-16]. In eukaryotes, NMD regulating factors, including three interacting 29 proteins, UPF1, UPF2 (also known as NMD2), and UPF3, are encoded by highly conserved 30 genes originally identified in yeast [17].

1 A frameshifted gene is sometimes expressed through programmed translational 2 frameshifting [18-20] or translational readthrough [21]. Translational frameshifting occurs 3 in various organisms, from E. coli to mammals, whereby the ribosome is guided toward a 4 triplet codon that is shifted one position to the upstream (+1) or downstream (−1) [22]. In 5 yeast, maintenance is globally controlled by the ribosomal frameshifting process 6 and NMD [23]. Translational readthrough is a process wherein a nonsense mRNA is 7 translated by translating the PTCs into specific amino acids [24]. in upf genes 8 caused nonsense suppression and subsequent readthrough in yeast and 5-20 fold decreases 9 in the rates of NMD [25], suggesting a direct link between NMD, nonsense suppression, 10 and readthrough. The three Upf proteins all interact with Sup35, and Upf1 interact with a 11 second release factor, Sup45 (eRF1), and binding of an SMG-1-Upf1-eRF1-eRF3 (SURF) 12 complex to EJC triggers Upf1 phosphorylation and NMD [26]. Besides, the nonsense 13 suppression caused by upf mutations is additive to those by sup35 and sup45 mutations 14 [27], suggesting that nonsense suppression is a nonsense-mRNA processing pathway, an 15 alternative to NMD. In a word, although nonsense mRNAs are usually subject to NMD, 16 when NMD is inhibited, they can also be translated by ribosomal frameshifting or 17 translational readthrough. 18 2.2 RNA can direct DNA repair 19 All types of RNAs are subject to either translation, degradation, or processing, and a 20 variety of molecular/cellular mechanisms are involved in RNA processing [28]. In the last 21 few decades, a link between DNA repair and RNA processing has been established. For 22 example, several functional proteins respond to DNA damage, and base-excision repair 23 , such as SMUG1, APE1, and PARP1, have been shown to participate in RNA 24 surveillance and processing [29]. 25 In eukaryotes, RNA is transcribed in the nucleus and transported to the cytoplasm [30]. 26 Recently, there is growing evidence that RNAs can also be transported back to the nucleus 27 to repair DNA double-strand breaks (DSBs), a process known as RNA-directed DNA Repair 28 [31-33]. In yeast [33], bacteria, and human embryonic kidney cells [34], a synthetic 29 DNA/RNA hybrid or an RNA-only oligonucleotide can serve as the template for repairing 30 DSB in a homologous DNA. In E. coli, small RNA patches can direct DNA modification 31 [35]. Here it is shown that mRNA could be edited and direct the repair of a frameshift

1 mutation in its CDS. Four deaminase genes (codA, cdd, add, and tadA) and the mismatch 2 repair pathways were upregulated in the frameshift or the revertant. Therefore, mismatch 3 repair and RNA editing are probably both involved in the frame repair. 4 2.3 RNA editing is linked to DNA repair 5 RNA editing is widely existing in E. coli [36], plants [37], humans [38-40], and 6 mammals [41]. There are several different forms of RNA editing, such as A-to-I editing 7 [42], C-to-U editing [43], and the insertion/deletion of uridine [44], but the schematism are 8 highly conserved among species, from bacteria to human. In particular, the nonsense apoB 9 mRNA editing complex suppresses its NMD, suggesting that nonsense mRNAs can be

10 subjected to RNA editing, which is linked to the NMD pathway [45]. 11 Both DNA mismatch repair and RNA editing involve deamination, removing an amine 12 group from a DNA/RNA molecule. Enzymes that catalyze this reaction are called 13 DNA/RNA deaminases. Cytidine deamination was first recognized as a mechanism for 14 RNA editing in wheat [46]. The tRNA-specific adenosine deaminases (ADATs) and the 15 cytidine/adenosine deaminases (CDARs/ADARs) belong to a superfamily of RNA 16 dependent deaminases [47]. Site-specific cytidine deamination introduces a stop codon 17 (UAA) into the edited apolipoprotein mRNA [48]. It is well known that deamination and 18 RNA editing play many important roles. In eukaryotes, studies have provided evidence that 19 deamination is related to both DNA repair and RNA editing. For example, V, 20 an RNA editing highly conserved from E. coli to human [49], is involved in 21 excision repair that removes deoxyinosine from DNA. Dysregulated RNA editing 22 contributes to genome instability in cancer cells [50]. 23 In E. coli, CodA catalyzes the hydrolytic deamination of cytosine to uracil, and the 24 isoguanine, the oxidation product of adenine and isocytosine [51, 52]; Cdd scavenges 25 cytidine and 2'-deoxycytidine for uridine monophosphate synthesis [53-55]; Add is an 26 enzyme that converts adenine, adenosine, and deoxyadenosine to guanine [56, 57]; in 27 eukaryotes, the cytosine deaminase (CDA) [58], the cytidine/deoxycytidine deaminase 28 (APOBEC1) [36, 59], and the adenosine deaminase (ADAR1 and ADAR2) [60-62] are all 29 responsible for RNA editing. 30 The tRNA-specific adenosine deaminase (TadA) was first identified in yeast [63] and 31 is also a prokaryotic RNA editing enzyme that was reported first in E. coli [64]. TadA is

1 also related to the eukaryotic RNA editing enzymes, ADAR1/ADAR2, which is widely 2 existing in many eukaryotic species, such as humans [65], mouse [66], and fruit fly [67]. 3 TadA, a prokaryotic deaminase for RNA editing first identified in E. coli, displays sequence 4 similarity to the yeast tRNA deaminase subunit Tad2p [64]. Besides, cytidine deaminase 5 (CodA) has been used as a molecular model for RNA editing and RNA substrate 6 recognition [36]. Altogether, these studies suggest that RNA editing is highly conserved 7 between and eukaryotes. Also, there is a direct link between the regulation of 8 mismatch repair and RNA editing, supporting that both mismatch repair and RNA editing 9 are involved in the frame repair. 10

1

2 3. Supplementary tables

3 Table S1. The number of changes in the DNA or RNA manipulating genes by comparing Fs, Rs, 4 and Rf with Wt (see Table S2-S12 for the regulated genes in each pathway)

Total changes Great changes Moderate changes Total Total (>=1.2 fold) (>=2.0 fold) (1.2-2.0-fold) genes comparisons up down up down up down DNA Replication 18 54 16 2 3 0 13 2 Transcription 8 24 9 4 0 0 9 4 RNA degradation 16 48 25 2 5 0 20 2 Nucleotide Excision Repair 8 24 12 1 0 0 12 1 Base Excision Repair 14 42 4 5 0 0 4 5 Mismatch Repair 23 69 17 7 2 0 15 7 Recombination 28 84 29 7 6 1 23 6 RNA editing 10 30 7 3 2 0 5 3 tRNA synthetases 80 240 71 16 3 1 68 24 RNA processing 50 150 29 18 5 0 24 18 Translation 60 180 24 102 3 16 21 86 Total (exclude translation) 255 765 219 65 26 2 193 72 Total (include translation) 315 945 243 167 29 18 214 158 5

1

2 Table S2. The changes in the DNA replication pathways by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b1842 159.90 112.16 125.42 141.16 ------holE DNA polymerase III subunit theta b0215 170.54 190.38 125.74 165.32 ------↓ -- dnaQ DNA polymerase III subunit epsilon b0184 66.08 116.03 87.85 93.12 ↑ ↑ ↑ -- ↓ dnaE DNA polymerase III subunit alpha b0470 121.51 156.36 152.15 158.94 ↑ ↑ ↑ -- -- dnaX DNA polymerase III subunit tau b1099 40.46 69.92 65.39 62.11 ↑ ↑ ↑ -- -- holB DNA polymerase III subunit delta'. b0640 37.00 83.50 82.68 56.94 ↑↑ ↑↑ ------holA DNA polymerase III subunit delta b4372 100.80 126.11 61.87 135.62 ------↓ -- holD DNA polymerase III subunit psi b4259 64.79 69.41 55.30 64.80 ------holC DNA polymerase III subunit chi b3701 137.09 174.00 159.33 175.95 -- -- ↑ -- -- dnaN beta sliding clamp b4052 126.16 137.92 139.98 189.76 -- -- ↑ -- ↑ dnaB replicative DNA b3066 185.31 189.31 173.12 187.35 ------dnaG DNA b4059 791.00 533.29 695.11 644.55 ↓ -- -- ↑ -- ssb ssDNA-binding protein b0214 136.98 127.92 97.39 128.54 ------rnhA HI b0183 52.35 97.98 74.57 83.24 ↑ ------rnhB RNase HII b3863 149.99 126.42 174.69 139.64 -- ↑ -- ↑ -- polA DNA polymerase I b2411 71.96 74.97 80.18 68.76 ------ligA DNA b3647 23.85 15.74 21.94 10.57 -- -- ↓ -- -- ligB DNA ligase b0231 6.40 157.62 23.59 28.07 ↑↑ -- -- ↓↓ ↓↓ dinB DNA polymerase IV 3 4 5 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

1 Table S3. The changes in the RNA polymerase by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b1922 2.47 0.27 0.74 1.21 ------fliA RNA polymerase sigma 28 (sigma F) factor b2741 2,586.95 1,946.22 1,868.15 1,213.38 ↓ ↓ ↓ -- ↓ rpoS RNA polymerase sigma S (sigma 38) factor b3202 198.75 233.24 260.55 259.49 -- ↑ ↑ -- -- rpoN RNA polymerase sigma 54 (sigma N) factor b3295 4,782.59 3,990.28 2,754.60 4,265.86 -- ↓ -- ↓ -- rpoA RNA polymerase alpha subunit b3649 633.75 736.77 590.78 1,014.62 -- -- ↑ -- ↑ rpoZ RNA polymerase omega subunit b3987 658.35 844.08 848.12 930.53 ↑ ↑ ↑ -- -- rpoB RNA polymerase beta subunit b3988 635.27 825.14 881.82 906.31 ↑ ↑ ↑ -- -- rpoC RNA polymerase beta prime subunit b4293 45.59 72.95 76.15 77.16 ------fecI RNA polymerase sigma-19 factor 2 3 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

1 2 Table S4. The changes in the RNA degradation pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b2830 484.58 333.42 360.63 384.86 ↓ ------rppH RNA pyrophosphohydrolase b1084 217.99 339.27 357.25 312.34 ↑ ↑ ↑ -- -- rne ribonuclease E b3780 381.39 408.22 463.69 538.39 -- ↑ ↑ -- ↑ rhlB ATP-dependent RNA helicase RhlB b2779 317.56 642.64 730.83 727.81 ↑↑ ↑↑ ↑↑ ↑ -- eno enolase b3164 886.73 925.08 954.49 967.27 -- ↑ ------pnp polynucleotide b0797 28.36 53.78 29.77 80.35 ↑ -- ↑↑ ↓ ↑ rhlE ATP-dependent RNA helicase RhlE b4179 198.74 197.25 172.61 232.92 -- -- ↑ -- -- rnr RNase R b3162 405.05 663.10 448.47 854.50 ↑ -- ↑↑ ↓ ↑ deaD ATP-dependent RNA helicase DeaD b3822 41.24 45.05 59.08 58.12 -- ↑ ↑ -- -- recQ ATP-dependent DNA helicase RecQ b3783 949.48 1,440.18 1,175.19 1,447.95 ↑ ↑ ↑ -- -- rho transcription termination factor Rho b3916 302.97 338.55 309.10 326.10 ------pfkA 6- I b0014 537.27 441.40 528.59 936.60 -- -- ↑ ↑ ↑↑ dnaK chaperone protein DnaK b4143 1,187.84 794.90 1,139.53 1,971.73 ↓ -- ↑ ↑ ↑↑ groL chaperonin GroEL b4172 2,403.91 2,004.11 1,774.57 2,712.58 -- -- ↑ -- ↑ hfq RNA-binding protein Hfq b2501 60.40 72.55 96.75 71.79 -- ↑ -- ↑ -- ppk polyphosphate b0143 184.82 261.57 166.04 252.07 ↑ -- ↑ ↓ -- pcnB poly(A) polymerase I 3 4 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

5

1 Table S5. The changes in the Nucleotide Excision Repair pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b1114 43.89 52.44 70.37 75.78 -- ↑ ↑ ↑ ↑ mfd transcription-repair coupling factor b4058 114.36 168.96 196.18 172.82 ↑ ↑ ↑ -- -- uvrA excision subunit A b0779 118.30 155.32 169.32 132.72 ↑ ↑ ------uvrB excision nuclease subunit b1913 39.04 70.35 63.80 55.65 ↑ ↑ ↑ -- -- uvrC excision nuclease subunit ssDNA and dsDNA helicase b3813 131.27 149.09 138.27 160.66 -- -- ↑ -- -- uvrD DNA helicase II b3863 149.99 126.42 174.69 139.64 -- ↑ -- ↑ -- polA DNA polymerase I b2411 71.96 74.97 80.18 68.76 ------ligA DNA ligase b3647 23.85 15.74 21.94 10.57 -- -- ↓ -- -- ligB DNA ligase 2 3 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change 4

1

2 Table S6. The changes in the Base Excision Repair pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b3635 36.39 24.23 28.57 41.55 ------mutM DNA-formamidopyrimidine glycosylase b0714 26.91 39.65 40.15 36.99 ------nei endonuclease VIII b1633 20.38 35.80 26.39 34.54 ------nth endonuclease III b2068 28.24 26.59 26.63 29.57 ------alkA DNA-3-methyladenine glycosylase 2 b3549 58.88 43.85 49.18 42.97 ------tag 3-methyl-adenine DNA glycosylase I, constitutive b3068 295.96 219.51 170.04 220.11 ↓ ↓ ↓ -- -- mug stationary phase mismatch/uracil DNA glycosylase b2580 112.98 88.47 70.92 116.75 -- ↓ ------ung uracil-DNA glycosylase b2961 52.78 68.97 60.90 84.12 -- -- ↑ -- -- mutY adenine DNA glycosylase b1749 137.97 136.94 104.86 132.67 ------xthA III b2159 81.34 83.73 94.71 99.17 ------nfo endonuclease IV b3863 149.99 126.42 174.69 139.64 -- ↑ -- ↑ -- polA DNA polymerase I b2892 71.07 95.99 82.32 102.17 ↑ -- ↑ -- -- recJ ssDNA-specific RecJ b2411 71.96 74.97 80.18 68.76 ------ligA DNA ligase b3647 23.85 15.74 21.94 10.57 -- -- ↓ -- -- ligB DNA ligase 3

4 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change 5

1 Table S7. The changes in the Mismatch Repair pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b2733 89.07 86.96 100.67 93.92 ------mutS DNA mismatch repair protein MutS b4170 55.45 75.62 63.57 77.37 ↑ -- ↑ -- -- mutL DNA mismatch repair protein MutL b2831 61.25 62.87 50.69 56.86 ------mutH DNA mismatch repair protein MutH b3813 131.27 149.09 138.27 160.66 -- -- ↑ -- -- uvrD ssDNA translocase and dsDNA helicase - DNA helicase II b2011 60.19 69.41 77.81 73.14 ------sbcB exodeoxyribonuclease I b2509 62.95 65.14 83.75 81.14 ------xseA exodeoxyribonuclease VII subunit XseA b0422 748.31 584.81 532.88 442.02 -- ↓ ↓ -- -- xseB exodeoxyribonuclease VII subunit XseB b1844 104.99 115.16 91.13 120.72 ------exoX exonuclease X b2892 71.07 95.99 82.32 102.17 ↑ -- ↑ -- -- recJ ssDNA-specific exonuclease RecJ b4059 791.00 533.29 695.11 644.55 ↓ -- -- ↑ -- ssb ssDNA-binding protein b0184 66.08 116.03 87.85 93.12 ↑ ↑ ↑ -- ↓ dnaE DNA polymerase III (DpoIII) subunit alpha b3701 137.09 174.00 159.33 175.95 -- -- ↑ -- -- dnaN beta sliding clamp b0470 121.51 156.36 152.15 158.94 ↑ ↑ ↑ -- -- dnaX DNA polymerase III (DpoIII) subunit tau b0640 37.00 83.50 82.68 56.94 ↑↑ ↑↑ ------holA DNA polymerase III (DpoIII) subunit delta b1099 40.46 69.92 65.39 62.11 ↑ ↑ ↑ -- -- holB DNA polymerase III (DpoIII) subunit delta'. b0215 170.54 190.38 125.74 165.32 ------↓ -- dnaQ DNA polymerase III (DpoIII) subunit epsilon b1842 159.90 112.16 125.42 141.16 ------holE DNA polymerase III (DpoIII) subunit theta b4259 64.79 69.41 55.30 64.80 ------holC DNA polymerase III (DpoIII) subunit chi b4372 100.80 126.11 61.87 135.62 ------↓ -- holD DNA polymerase III (DpoIII) subunit psi b2411 71.96 74.97 80.18 68.76 ------ligA DNA ligase b3647 23.85 15.74 21.94 10.57 -- -- ↓ -- -- ligB DNA ligase b3387 49.65 61.44 68.81 65.83 ------dam DNA adenine methyltransferase b3068 295.96 219.51 170.04 220.11 ↓ ↓ ↓ -- -- mug stationary phase mismatch/uracil DNA glycosylase 2 3 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change 4

1

2 Table S8. The changes in the Homologous Recombination pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs Gene Description b2892 71.07 95.99 82.32 102.17 ↑ -- ↑ -- -- recJ ssDNA-specific exonuclease RecJ b4059 791.00 533.29 695.11 644.55 ↓ -- -- ↑ -- ssb ssDNA-binding protein b3700 26.95 48.98 43.10 49.03 ↑ -- ↑ -- -- recF DNA repair protein RecF b2565 16.56 29.08 30.53 33.01 ------recO DNA repair protein RecO b0472 97.58 174.91 136.43 166.60 ↑ -- ↑ -- -- recR DNA repair protein RecR b2616 26.71 139.48 37.52 52.98 ↑↑ -- ↑↑ ↓↓ ↓↓ recN recombination and repair protein b2699 933.87 1,370.65 730.25 1,047.19 ↑ -- ↑ ↓ ↓ recA DNA recombination/repair protein RecA b3863 149.99 126.42 174.69 139.64 -- ↑ -- ↑ -- polA DNA polymerase I (DpoI) b1861 190.64 146.25 108.82 112.54 -- ↓ ↓ -- -- ruvA Holliday junction branch migration complex subunit, RuvA b1860 87.65 111.83 94.36 86.58 ------ruvB Holliday junction branch migration complex subunit, RuvB b1863 75.18 110.55 106.26 156.33 -- -- ↑↑ -- -- ruvC crossover junction RuvC b3652 12.71 18.67 20.36 26.05 -- -- ↑ -- -- recG ATP-dependent DNA helicase RecG b2820 15.94 24.93 31.06 27.71 ↑ ↑↑ ↑ -- -- recB exodeoxyribonuclease V subunit RecB b2822 28.78 31.87 40.90 33.12 -- ↑ ------recC exodeoxyribonuclease V subunit RecC b2819 22.55 27.61 27.07 27.39 ------recD exodeoxyribonuclease V subunit RecD b0184 66.08 116.03 87.85 93.12 ↑ ↑ ↑ -- ↓ dnaE DNA polymerase III (DpoIII) subunit alpha b3701 137.09 174.00 159.33 175.95 -- -- ↑ -- -- dnaN beta sliding clamp b0470 121.51 156.36 152.15 158.94 ↑ ↑ ↑ -- -- dnaX DNA polymerase III (DpoIII) subunit tau b0640 37.00 83.50 82.68 56.94 ↑↑ ↑↑ ------holA DNA polymerase III (DpoIII) subunit delta b1099 40.46 69.92 65.39 62.11 ↑ ↑ ↑ -- -- holB DNA polymerase III (DpoIII) subunit delta’. b0215 170.54 190.38 125.74 165.32 ------↓ -- dnaQ DNA polymerase III (DpoIII) subunit epsilon b1842 159.90 112.16 125.42 141.16 ------holE DNA polymerase III (DpoIII) subunit theta b4259 64.79 69.41 55.30 64.80 ------holC DNA polymerase III (DpoIII) subunit chi b4372 100.80 126.11 61.87 135.62 ------↓ -- holD DNA polymerase III (DpoIII) subunit psi b3935 26.89 23.65 22.90 31.40 ------priA primosome factor N'

b4201 1,837.23 1,116.01 627.55 1,311.36 ↓ ↓↓ ↓ ↓ -- priB primosomal replication protein N b0467 104.26 110.41 59.22 106.67 -- ↓ -- ↓ -- priC primosomal replication protein N'‘. b4362 102.60 121.04 91.27 103.98 ------dnaT primosomal protein DnaT 1

2 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change 3

1

2 Table S9. The changes in the RNA editing pathway by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs Gene Description b0324 - 48.82 - - ↑↑ -- -- ↓↓ ↓↓ yahJ putative Metallo-dependent domain deaminase b0337 - 48.76 - - ↑↑ -- -- ↓↓ ↓↓ codA cytosine/isoguanine deaminase b1623 224.72 282.87 377.11 191.6 ↑ ↑ -- ↑ ↓ add adenosine deaminase b1809 424.13 340.22 302.62 398.27 -- ↓ ------yoaB putative reactive intermediate deaminase b2065 472.63 410.44 419.79 522.81 ------↑ dcd deoxycytidine triphosphate deaminase dCTP deaminase b2143 68.82 48.13 66.27 114.28 -- -- ↑ -- ↑↑ cdd cytidine/deoxycytidine deaminase b2559 50.74 56.47 41.01 68.16 ------tadA tRNA-specific adenosine deaminase b2883 8.21 6.99 5.62 5.42 ------guaD guanine deaminase b3113 31.42 36.74 89.69 79.58 -- ↑ ↑ ↑ ↑ tdcF putative reactive intermediate deaminase b3665 48.74 39.43 28.19 24.28 -- ↓ ↓ -- ↓ adeD cryptic adenine deaminase 3

4 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change 5

1

2 Table S10. The changes in the tRNA synthetases by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b0026 306.93 419.6 301.51 369.16 ↑ -- ↑ ↓ -- ileS isoleucyl-tRNA synthetase b0058 23.95 50.26 35.6 42.8 ↑ ------rluA dual specificity 23S rRNA pseudouridine(746) tRNA b0144 40.8 49.76 43.83 42.89 ------gluQ glutamyl-Q tRNA (Asp) synthetase b0188 61.38 74.49 51.81 68.32 ------tilS tRNA (Ile)-lysidine synthetase b0191 39.88 30.16 20.05 26.38 ------arfB alternative stalled-ribosome rescue factor peptidyl-tRNA b0194 309.7 542.15 355.68 494.7 ↑ ↑ ↑ ↓ -- proS prolyl-tRNA synthetase b0195 18.06 46.02 34.68 53.44 ↑ -- ↑ -- -- tsaA tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase SAM-dependent b0405 75.28 93.47 66.31 98.66 ------queA S-adenosylmethionine:tRNA ribosyltransferase- b0406 169.86 286.77 202.34 292.16 ↑ -- ↑ ↓ -- tgt tRNA -guanine transglycosylase b0423 84.07 113.79 89.61 148.74 ↑ -- ↑ -- ↑ thiI tRNA s(4)U8 sulfurtransferase b0481 52.16 72.79 41.96 63.94 ------ybaK Cys-tRNA (Pro)/Cys-tRNA (Cys) deacylase b0503 31.3 36.57 27.43 33.12 ------mnmH tRNA 2-selenouridine synthase selenophosphate-dependent b0526 130.04 127.6 110.89 182.04 -- -- ↑ -- ↑ cysS cysteinyl-tRNA synthetase b0642 315.69 438.23 358.17 338.07 ↑ ↑ -- -- ↓ leuS leucyl-tRNA synthetase b0661 252.85 270.25 188.68 309.7 -- -- ↑ ↓ -- miaB tRNA -i(6)A37 methylthiotransferase b0680 176.19 171.88 190.77 180.76 ------glnS glutamyl-tRNA synthetase b0885 38.54 43.71 46.61 46 ------aat leucyl/phenylalanyl-tRNA -protein b0893 609.37 639.09 755.81 748.31 -- ↑ ↑ ↑ -- serS seryl-tRNA synthetase b0930 358.2 450.29 490 540.03 ↑ ↑ ↑ -- ↑ asnS asparaginyl tRNA synthetase b0969 121.08 120.15 103.85 147.42 ------tusE mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase b1133 262.28 336.36 324.27 421.98 ↑ ↑ ↑ -- ↑ mnmA tRNA (Gln CLys CGlu) U34 2-thiouridylase b1204 185.77 118.44 109.92 153.21 ↓ ↓ ------pth peptidyl-tRNA hydrolase b1210 195.52 211.12 186.07 208.77 ------hemA glutamyl tRNA reductase b1285 14.75 30.14 22.77 8.69 ↑ ------↓↓ gmr cyclic-di-GMP csgD regulator b1344 123.89 96.88 84.74 124.26 -- ↓ ------ttcA tRNA s(2)C32 thioltransferase iron sulfur cluster protein

b1637 373.4 321.29 364.12 383.75 ------↑ tyrS tyrosyl-tRNA synthetase b1713 190.52 245.27 267.5 249.5 ↑ ↑ ↑ -- -- pheT phenylalanine tRNA synthetase beta subunit b1714 160.25 179.93 167.86 194.92 ------pheS phenylalanine tRNA synthetase alpha subunit b1715 122.33 69.79 51.03 112.37 ------pheM phenylalanyl-tRNA synthetase operon leader peptide b1719 1,539.10 1,195.20 981.46 1,262.97 ↓ ↓ ------thrS threonyl-tRNA synthetase b1787 120.15 151.89 104.45 132.51 ------yeaK aminoacyl-tRNA editing domain protein b1807 95.93 94.76 114.22 119.25 ------tsaB tRNA (ANN) t(6)A37 threonylcarbamoyladenosine b1866 330.92 329.02 377.33 426.73 -- ↑ ↑ ↑ ↑ aspS aspartyl-tRNA synthetase b1871 34.16 67.24 55.25 64.04 ↑ ↑ ↑ -- -- cmoB tRNA (cmo5U34)-carboxymethyltransferase b1876 225.4 207.83 187.97 232.99 ------argS arginyl-tRNA synthetase b2114 146.67 191.26 203.32 245.01 ↑ ↑ ↑ -- ↑ metG methionyl-tRNA synthetase b2140 31.47 14.29 12.86 11.77 ↓ ↓ ↓ -- -- dusC tRNA -dihydrouridine synthase b2268 53.2 50.89 40.22 49.96 ------rbn RNase BN tRNA processing enzyme b2318 77.1 47.56 54.54 53.4 ↓ ------truA tRNA pseudouridine(38-40) synthase b2400 389.02 420.84 369.91 460.92 -- -- ↑ -- -- gltX glutamyl-tRNA synthetase b2474 16.56 26.58 23.66 20.33 ------tmcA elongator methionine tRNA (ac4C34) acetyltransferase b2514 362.68 396.88 401.25 428.19 -- -- ↑ -- -- hisS histidyl tRNA synthetase b2517 168.35 232.82 217.34 250.76 ↑ ↑ ↑ -- -- rlmN dual specificity 23S rRNA m(2)A2503 tRNA b2530 836.44 685.94 342.26 513.2 -- ↓↓ ↓ ↓ ↓ iscS cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent b2532 674.13 474.42 485.87 661.23 ↓ ↓ -- -- ↑ trmJ tRNA mC32 CmU32 2'-O-methyltransferase SAM-dependent b2559 50.74 56.47 41.01 68.16 ------tadA tRNA -specific adenosine deaminase b2575 56.06 45.75 43.57 60.96 ------trmN tRNA 1(Val) (adenine(37)-N6)-methyltransferase b2607 4,051.00 2,481.39 1,861.11 2,726.77 ↓ ↓ ↓ -- -- trmD tRNA m(1)G37 methyltransferase SAM-dependent b2697 375.34 449.79 493.98 510.45 ↑ ↑ ↑ -- -- alaS alanyl-tRNA synthetase b2745 110.44 126.37 101.12 135.68 ------truD tRNA (Glu) pseudouridine(13) synthase b2791 48.31 52.39 39.71 40.53 ------truC tRNA (Ile1 CAsp) pseudouridine(65) synthase tRNA threonylcarbamoyladenosine dehydratase b2812 101 62.02 58.89 58.34 ↓ ↓ ↓ -- -- tcdA sulfur acceptor for CsdA b2890 246.25 391.01 413.01 428.45 ↑ ↑ ↑ -- -- lysS lysine tRNA synthetase constitutive b2960 200.52 144.76 116.3 168.56 ↓ ↓ ------trmI tRNA m(7)G46 methyltransferase SAM-dependent

b3056 91.15 115.33 120.91 132.71 -- ↑ ↑ -- -- cca fused tRNA nucleotidyl transferase b3064 171.1 154.86 127.18 198.44 ------tsaD tRNA (ANN) t(6)A37 threonylcarbamoyladenosine b3074 33.6 37.13 22.81 49.22 ------ygjH putative tRNA binding protein putative tRNA corner chaperone b3166 140.18 202.1 178.34 240.61 ↑ ↑ ↑ -- -- truB tRNA pseudouridine synthase b3260 441.56 438.69 419.33 531.59 -- -- ↑ -- ↑ dusB tRNA -dihydrouridine synthase b3282 86.46 114.07 97.12 71.51 ------tsaC tRNA (ANN) t(6)A37 threonylcarbamoyladenosine b3343 37 42.94 46 45.41 ------tusB mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein b3344 18.74 13.63 17.17 15.5 ------tusC mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein b3345 28.45 41.08 47.47 36.5 ------tusD sulfurtransferase for 2-thiolation step b3384 174.75 181.63 190.72 220.52 -- -- ↑ -- -- trpS tryptophanyl-tRNA synthetase b3442 1.66 0.67 0.3 0.44 ------yhhZ putative Hcp1 family polymorphic toxin protein b3470 386.2 305.59 224.77 494.75 -- ↓ -- -- ↑ tusA mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase b3559 222.19 319.84 373.8 395.32 ↑ ↑ ↑ ↑ ↑ glyS glycine tRNA synthetase, beta subunit b3560 306.48 375.35 390.89 473.39 ↑ ↑ ↑ -- ↑ glyQ glycine tRNA synthetase, alpha subunit b3590 43.41 47.34 58.69 82.32 -- -- ↑↑ -- ↑ selB selenocysteinyl-tRNA-specific translation factor b3606 59.19 30.64 27.95 51.87 -- ↓ ------trmL tRNA Leu mC34 CmU34 2'-O-methyltransferase b3651 19.04 36.7 35.59 43.72 -- -- ↑ -- -- trmH tRNA mG18-2'-O-methyltransferase SAM-dependent b3706 80.01 81.68 72.09 87.5 ------mnmE tRNA U34 5-methylaminomethyl-2-thiouridine b3741 158.32 184.44 142.91 237.2 -- -- ↑ -- ↑ mnmG 5-methylaminomethyl-2-thiouridine modification at tRNA U34 b3887 78.65 54.67 61.31 60.51 ------dtd D-tyr-tRNA (Tyr) deacylase b3965 144.03 112.67 80.71 149.03 -- ↓ -- ↓ -- trmA tRNA m(5)U54 methyltransferase SAM-dependent b4049 251.31 180.59 182.61 264.41 ↓ ------↑ dusA tRNA -dihydrouridine synthase A b4129 130.2 306.45 207.26 524.48 ↑↑ ↑ ↑↑ ↓ ↑ lysU lysine tRNA synthetase, heat-inducible b4168 33.82 46.73 35.56 47.18 ------tsaE tRNA (ANN) t(6)A37 threonylcarbamoyladenosine b4171 460.47 627.65 516.78 787.5 ↑ -- ↑ -- ↑ miaA delta(2)-isopentenylpyrophosphate tRNA -adenosine transferase b4258 203.57 261.43 236.72 319.98 ↑ ↑ ↑ -- ↑ valS valyl-tRNA synthetase 1

2 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

1

2 Table S11. The changes in the RNA processing pathways by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b0059 28.59 56.31 41.81 45.35 ↑↑ ↑ ↑ ↓ -- rapA RNA polymerase remodeling/recycling factor ATPase b0069 26.16 30.34 23.58 29.17 ------sgrR transcriptional DNA -binding transcriptional activator of sgrS sRNA b0147 24.75 29.57 23.95 24.3 ------ligT 2'-5' RNA ligase b0183 52.35 97.98 74.57 83.24 ↑ ------rnhB ribonuclease HII degrades RNA of DNA -RNA hybrids b0214 136.98 127.92 97.39 128.54 ------rnhA ribonuclease HI degrades RNA of DNA -RNA hybrids b0225 135.57 116.08 70.28 98.75 -- ↓ ------yafQ mRNA interferase toxin of toxin-antitoxin pair YafQ/DinJ b0233 3.56 28.04 0.89 2.19 ↑ -- -- ↓ ↓ yafO mRNA interferase toxin of the YafO-YafN toxin-antitoxin system b0528 22.51 19.35 11.61 18.01 ------ybcJ ribosome-associated protein putative RNA -binding protein b0623 24,920.95 28,949.78 27,107.59 19,381.45 -- ↑ ↓ -- ↓ cspE constitutive cold shock family, transcription antitermination protein b0797 28.36 53.78 29.77 80.35 ↑ -- ↑↑ ↓ ↑ rhlE ATP-dependent RNA helicase b1045 48.88 54.4 64.51 37.55 ------ymdB O-acetyl-ADP-ribose deacetylase RNase III inhibitor b1084 217.99 339.27 357.25 312.34 ↑ ↑ ↑ -- -- rne RNA -binding protein RNA degradosome b1267 138.69 111.26 99.57 134.5 ------yciO putative RNA binding protein b1285 14.75 30.14 22.77 8.69 ↑ ------↓↓ gmr cyclic-di-GMP phosphodiesterase csgD regulator b1652 64.95 78.76 69.79 79.65 ------rnt RNase T T structured DNA 3' exonuclease b1831 832 883.41 746.81 988.34 -- -- ↑ -- -- proQ RNA chaperone putative ProP translation regulator b1844 104.99 115.16 91.13 120.72 ------exoX exodeoxyribonuclease 10 DNA exonuclease X b2184 19.36 20.62 21.87 20.89 ------yejH putative ATP-dependent DNA or RNA helicase b2501 60.4 72.55 96.75 71.79 -- ↑ -- ↑ -- ppk component of the RNA degradosome b2610 544.21 458.71 486.52 606.58 ------↑ ffh Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) b2620 319.86 232.86 261.15 376.9 ↓ ------↑ smpB tmRNA -binding trans-translation protein b2630 217.76 156.62 99.51 155.05 ↓ ↓ ↓ ↓ -- rnlA CP4-57 prophage RNase LS b2666 17.87 66.66 36.66 38.38 ------yqaE cyaR sRNA -regulated protein b2754 30.53 11.02 10.54 6.12 -- -- ↓ -- -- ygbF CRISPR adaptation ssRNA endonuclease

b2756 8.88 8.18 4.42 6.39 ------casE CRISPR RNA precursor cleavage enzyme CRISP RNA (crRNA ) b2757 7.63 7.27 4.71 3.62 ------casD CRISP RNA (crRNA ) containing Cascade antiviral complex protein b2758 7.32 7.01 5.66 4.63 ------casC CRISP RNA (crRNA ) containing Cascade antiviral complex protein b2759 6.62 4.06 2.19 5.78 ------casB CRISP RNA (crRNA ) containing Cascade antiviral complex protein b2760 6.24 4.94 1.29 1.85 -- ↓ ------casA CRISP RNA (crRNA ) containing Cascade antiviral complex protein b2782 22.2 45.57 25.24 18.68 ------mazF mRNA interferase toxin antitoxin is MazE b2830 484.58 333.42 360.63 384.86 ↓ ------rppH RNA pyrophosphohydrolase b3022 77.13 249.81 19.03 32.29 ↑↑ ↓ ↓ ↓↓ ↓↓ mqsR GCU-specific mRNA interferase toxin of the MqsR-MqsA b3083 20.29 16.82 4.49 9.41 ------higB mRNA interferase toxin of the HigB-HigA toxin-antitoxin system b3162 405.05 663.1 448.47 854.5 ↑ -- ↑↑ ↓ ↑ deaD ATP-dependent RNA helicase b3180 960.37 938.02 1,118.23 1,511.19 -- -- ↑ -- ↑ yhbY RNA binding protein associated with pre-50S ribosomal subunits b3205 89.31 126.95 158.06 141.74 ↑ ↑↑ ↑ -- -- yhbJ adaptor protein for GlmZ/GlmY sRNA decay b3229 1,199.97 998 1,017.64 1,345.83 -- -- ↑ -- ↑ sspA stringent starvation protein phage P1 late gene activator b3252 67.15 65.02 60.61 72.68 ------csrD targeting factor for csrBC sRNA degradation b3421 22.72 15.52 12.09 11.51 -- -- ↓ -- -- rtcB RNA -splicing ligase b3556 81,944.30 66,608.84 81,277.95 129,310.02 -- -- ↑ ↑ ↑ cspA RNA chaperone and antiterminator cold-inducible b3704 67.09 96.51 100.11 150.15 -- -- ↑ -- -- rnpA protein C5 component of RNase P b3780 381.39 408.22 463.69 538.39 -- ↑ ↑ -- ↑ rhlB ATP-dependent RNA helicase b3929 1,947.51 955.16 1,298.03 1,578.28 ↓ ↓ -- ↑ ↑ rraA ribonuclease E (RNase E) inhibitor protein b3995 471.31 316.44 388.5 360.43 ↓ -- ↓ -- -- rsd stationary phase protein binds sigma 70 RNA polymerase subunit b4128 4.19 1.98 0.59 0.59 ------ghoS antitoxin of GhoTS toxin-antitoxin pair endonuclease b4172 2,403.91 2,004.11 1,774.57 2,712.58 -- -- ↑ -- ↑ hfq global sRNA chaperone HF-I host factor b4179 198.74 197.25 172.61 232.92 -- -- ↑ -- -- rnr exoribonuclease R RNase R b4255 1,389.96 1,005.89 1,414.53 1,726.12 ↓ -- ↑ ↑ ↑ rraB protein inhibitor of RNase E b4331 83.51 58.71 42.97 85.46 -- ↓ ------kptA RNA 2'- b4475 22.52 17.37 12.85 16.12 ------rtcA RNA 3'-terminal phosphate cyclase 1

2 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

1 Table S12. The changes in ribosomal proteins and elongation factors by comparing Fs, Rs, Rf, and Wt.

FPKM Comparison Gene_id Gene Description Wt Fs Rs Rf Fs-Wt Rs-Wt Rf-Wt Rs-Fs Rf-Fs b0911 4,881.80 4,329.23 2,915.26 4,615.03 -- ↓ -- ↓ -- rpsA 30S ribosomal subunit protein S1 b0169 5,210.67 5,638.12 2,769.82 5,580.26 -- ↓ -- ↓ -- rpsB 30S ribosomal subunit protein S2 b3314 6,001.73 4,246.63 2,606.57 4,780.97 ↓ ↓ -- ↓ -- rpsC 30S ribosomal subunit protein S3 b3296 5,306.18 3,213.22 2,401.51 3,520.50 ↓ ↓ ↓ ↓ -- rpsD 30S ribosomal subunit protein S4 b3303 5,219.52 3,714.18 2,514.56 4,122.91 ↓ ↓ -- ↓ -- rpsE 30S ribosomal subunit protein S5 b4200 11,237.63 7,208.42 5,210.04 10,515.37 ↓ ↓ -- ↓ ↑ rpsF 30S ribosomal subunit protein S6 b3341 2,787.97 3,276.46 1,991.64 4,018.87 ↑ ↓ ↑ ↓ ↑ rpsG 30S ribosomal subunit protein S7 b3306 4,977.60 3,348.79 2,361.72 3,394.19 ↓ ↓ ↓ ↓ -- rpsH 30S ribosomal subunit protein S8 b3230 3,231.65 4,069.99 2,615.69 5,751.05 ↑ -- ↑ ↓ ↑ rpsI 30S ribosomal subunit protein S9 b3321 22,467.02 13,936.05 9,627.80 15,731.15 ↓ ↓↓ ↓ ↓ -- rpsJ 30S ribosomal subunit protein S10 b3297 3,177.73 1,869.21 1,464.44 1,955.16 ↓ ↓ ↓ -- -- rpsK 30S ribosomal subunit protein S11 b3342 5,673.02 6,743.22 4,115.87 8,204.61 ↑ -- ↑ ↓ ↑ rpsL 30S ribosomal subunit protein S12 b3298 4,492.67 3,143.27 2,213.90 3,229.96 ↓ ↓ ↓ ↓ -- rpsM 30S ribosomal subunit protein S13 b3307 7,059.01 4,755.04 3,306.83 4,364.90 ↓ ↓ ↓ ↓ -- rpsN 30S ribosomal subunit protein S14 b3165 12,132.52 8,313.65 7,112.08 13,508.37 ↓ ↓ -- -- ↑ rpsO 30S ribosomal subunit protein S15 b2609 5,413.63 3,419.57 3,122.36 4,268.17 ↓ ↓ -- -- ↑ rpsP 30S ribosomal subunit protein S16 b3311 2,210.32 2,002.85 965.72 2,191.57 -- ↓ -- ↓ -- rpsQ 30S ribosomal subunit protein S17 b4202 437.71 564.74 233.22 635.53 -- ↓ ↑ ↓↓ -- rpsR 30S ribosomal subunit protein S18 b3316 4,119.94 2,301.92 1,226.47 2,079.92 ↓ ↓↓ ↓ ↓ -- rpsS 30S ribosomal subunit protein S19 b0023 4,072.86 5,394.79 5,076.88 8,211.16 ↑ ↑ ↑↑ -- ↑ rpsT 30S ribosomal subunit protein S20 b3065 6,413.36 6,892.60 7,728.74 10,755.13 -- ↑ ↑ ↑ ↑ rpsU 30S ribosomal subunit protein S21 b3984 6,103.14 4,581.04 2,863.10 5,969.33 ↓ ↓ -- ↓ ↑ rplA 50S ribosomal subunit protein L1 b3317 6,337.07 4,698.36 2,991.13 5,119.89 ↓ ↓ -- ↓ -- rplB 50S ribosomal subunit protein L2 b3320 7,454.33 6,288.82 4,150.88 6,857.93 -- ↓ -- ↓ -- rplC 50S ribosomal subunit protein L3 b3319 5,038.70 3,948.32 2,498.27 4,141.10 ↓ ↓ -- ↓ -- rplD 50S ribosomal subunit protein L4 b3308 4,410.18 4,447.61 2,841.56 4,613.33 -- ↓ -- ↓ -- rplE 50S ribosomal subunit protein L5

b3305 4,552.18 3,194.18 2,148.00 3,513.49 ↓ ↓ ↓ ↓ -- rplF 50S ribosomal subunit protein L6 b3986 13,058.77 8,926.02 5,092.16 14,120.49 ↓ ↓↓ -- ↓ ↑ rplL 50S ribosomal subunit protein L12 b4203 2,492.01 3,476.38 2,210.96 5,343.81 ↑ -- ↑↑ ↓ ↑ rplI 50S ribosomal subunit protein L9 b3985 12,894.73 7,521.79 4,063.46 9,987.31 ↓ ↓↓ ↓ ↓ ↑ rplJ 50S ribosomal subunit protein L10 b3983 5,281.39 3,632.83 2,258.66 4,716.88 ↓ ↓↓ -- ↓ ↑ rplK 50S ribosomal subunit protein L11 b3231 9,684.41 6,314.89 4,156.59 8,192.87 ↓ ↓↓ -- ↓ ↑ rplM 50S ribosomal subunit protein L13 b3310 12,197.98 7,839.69 5,939.85 9,373.70 ↓ ↓ ↓ -- ↑ rplN 50S ribosomal subunit protein L14 b3301 4,621.93 3,765.91 2,659.19 4,165.60 -- ↓ -- ↓ -- rplO 50S ribosomal subunit protein L15 b3313 4,454.14 2,679.18 1,515.55 2,969.78 ↓ ↓↓ ↓ ↓ -- rplP 50S ribosomal subunit protein L16 b3294 3,115.94 3,442.61 2,294.70 4,595.33 -- -- ↑ ↓ ↑ rplQ 50S ribosomal subunit protein L17 b3304 3,463.77 2,540.58 1,638.32 2,575.63 ↓ ↓ ↓ ↓ -- rplR 50S ribosomal subunit protein L18 b2606 3,761.28 2,610.89 1,906.68 3,320.01 ↓ ↓ -- ↓ ↑ rplS 50S ribosomal subunit protein L19 b1716 6,859.38 7,758.93 4,163.07 8,864.45 -- ↓ ↑ ↓ -- rplT 50S ribosomal subunit protein L20 b3186 3,981.84 2,691.33 2,539.44 4,506.75 ↓ ↓ ↑ -- ↑ rplU 50S ribosomal subunit protein L21 b3315 4,123.22 3,258.41 1,780.89 3,293.10 ↓ ↓↓ -- ↓ -- rplV 50S ribosomal subunit protein L22 b3318 6,497.71 3,348.46 2,008.53 2,979.80 ↓ ↓↓ ↓↓ ↓ -- rplW 50S ribosomal subunit protein L23 b3309 4,845.90 3,252.68 2,153.53 3,016.29 ↓ ↓ ↓ ↓ -- rplX 50S ribosomal subunit protein L24 b2185 6,230.81 4,500.72 2,802.96 7,068.34 ↓ ↓ ↑ ↓ ↑ rplY 50S ribosomal subunit protein L25 b3185 4,542.69 3,340.60 2,608.09 5,462.19 ↓ ↓ ↑ -- ↑ rpmA 50S ribosomal subunit protein L27 b3637 12,798.35 9,145.76 6,655.57 12,464.02 ↓ ↓ -- ↓ ↑ rpmB 50S ribosomal subunit protein L28 b3312 597.48 219.80 81.89 127.14 ↓↓ ↓↓ ↓↓ ↓ -- rpmC 50S ribosomal subunit protein L29 b3302 147.00 77.42 20.61 39.72 -- ↓↓ ↓ ↓ -- rpmD 50S ribosomal subunit protein L30 b3936 19,592.77 12,202.68 9,576.80 18,996.32 ↓ ↓ -- -- ↑ rpmE 50S ribosomal subunit protein L31 b0296 - 2.23 ------ykgM putative ribosomal protein b1089 3,310.71 3,353.72 2,066.07 4,307.10 -- ↓ ↑ ↓ ↑ rpmF 50S ribosomal subunit protein L32 b3636 147.98 133.19 55.73 173.33 -- ↓ ------rpmG 50S ribosomal subunit protein L33 b3703 3,278.27 3,960.45 2,425.59 5,739.31 ↑ -- ↑ ↓ ↑ rpmH 50S ribosomal subunit protein L34 b1717 3,469.05 3,268.40 1,357.05 2,791.65 -- ↓↓ -- ↓↓ -- rpmI 50S ribosomal subunit protein L35 b3299 ------rpmJ 50S ribosomal subunit protein L36 b4506 - 1.39 ------ykgO putative ribosomal protein

b3590 43.41 47.34 58.69 82.32 -- -- ↑↑ -- ↑ selB selenocysteinyl-tRNA -specific translation factor b3339 26.52 15.24 12.67 14.71 -- ↓ ------tufA translation elongation factor EF-Tu 1 b3980 109.39 80.67 45.62 91.67 ↓ ↓↓ -- ↓ -- tufB translation elongation factor EF-Tu 2 b0170 2,420.23 2,735.05 1,536.00 2,736.68 -- ↓ ↑ ↓ -- tsf translation elongation factor EF-Ts 1

2 Note: One arrow: moderate (1.2-2.0-fold) changes; Two arrows: great (>=2.0 fold) changes; "--" no change

3

1 2 4. Reference cited in this supplementary material

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