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The Impact of Type VI Secretion System, Bacteriocins And bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 The impact of type VI secretion system, bacteriocins and antibiotics on competition 2 amongst Soft-Rot Enterobacteriaceae: Regulation of carbapenem biosynthesis by iron 3 and the transcriptional regulator Fur 4 Short title: Antimicrobial production by SRE and Fur-Fe2+ regulation of carbapenem 5 Divine Yutefar Shyntum1, Ntombikayise Nkomo1,2, Alessandro Rino Gricia1,2, Ntwanano 6 Luann Shigange1, Daniel Bellieny-Rabelo1 and Lucy Novungayo Moleleki1, 2* 7 1Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lunnon 8 Road, Pretoria, South Africa, 0028 9 2Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Lunnon Road, 10 Pretoria, South Africa, 0028 11 12 *Corresponding author 13 E-mail: [email protected] 14 Tel: +27(0)12 4204662 15 Fax: +27(0)12 4203266 16 1 bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 17 Abstract 18 Plant microbial communities’ complexity provide a rich model for investigation on biochemical and 19 regulatory strategies involved in interbacterial competition. Within these niches, the soft rot 20 Enterobacteriaceae (SRE) comprise an emerging group of plant-pathogens inflicting soft rot/black- 21 leg diseases and causing economic losses worldwide in a variety of crops. In this report, a range of 22 molecular and computational techniques are utilized to survey the contribution of antimicrobial 23 factors such as bacteriocins, carbapenem antibiotic and type VI secretion system (T6SS) in 24 interbacterial competition among plant-pathogens/endophytes using an aggressive SRE as a case 25 study (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 – Pcb1692). A preliminary 26 screening using next-generation sequencing of 16S rRNA comparatively analysing healthy and 27 diseased potato tubers, followed by in vitro competition assays, corroborated the aggressiveness of 28 Pcb1692 against several relevant taxa sharing this niche ranging from Proteobacteria to Firmicutes. 29 The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on 30 carbapenem or pyocin production. Whereas for targeted Firmicutes, only pyocin seems to play a role 31 in growth inhibition by Pcb1692. Further analyses elucidated that although T6SS confers no relevant 32 advantage during in vitro competition, a significant attenuation in competition by the mutant strain 33 lacking a functional T6SS was observed in planta. Furthermore, production of carbapenem by 34 Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, 35 upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex 36 regulatory mechanism involving these three genes. Potential Fur binding sites found upstream of slyA, 37 carR and expR in Pectobacterium genomes harboring carbapenem-associated genes further suggests a 38 conserved regulatory pattern in the genus, in which carbapenem might be modulated in response to 39 iron through the control exerted by Fur over secondary regulators. Furthermore, we unveiled the 40 striking role played by S-pyocin in growth inhibition within the SRE group. 41 42 Authors Summary 43 For many phytopathogenic bacteria, more is known about interactions within the host and virulence 44 factors used for host colonisation while relatively less is known about microbe-microbe interactions 45 and factors that shape niche colonisation. The soft rot Enterobacteriaceae (SRE) comprise an 46 emerging group of phytopathogens causing soft rot/black-leg diseases in a variety of crops leading to 47 huge economic losses worldwide. In this report, a range of molecular and computational techniques 48 are utilized to survey the contribution of antimicrobial factors such as bacteriocins, carbapenem 49 antibiotic and type VI secretion system (T6SS) in interbacterial competition among plant- 50 pathogens/endophytes using an aggressive SRE as a case study (Pcb1692). Our results show that 2 bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 51 Pcb1692 inhibits growth of other SRE and several potato endophytes using either the type VI 52 secretion, carbapenem or bacteriocins. Carbapenem plays a role in both inter and intrabacterial 53 competition in vitro, while the Pcb1692T6SS plays a role in interbacterial competition in planta (in 54 potato tubers). We also demonstrate that carbapenem regulation requires the presence of 55 environmental iron and oxygen in a complex network consisting of Pcb1692 Fur, SlyA, and ExpI. 56 The presence of these gene homologs in several SREs suggests that they too can deploy similar 57 antimicrobials to target other bacteria. 58 59 Introduction 60 For phytopathogenic bacteria, more is known about interactions within their hosts and virulence 61 factors that these microbes recruit to successfully colonise their hosts while relatively less is known 62 about microbe-microbe interactions and how such interactions impact on niche colonisations (1-4). 63 Studies on the mammalian gut microbiome, the advent of new sequencing technologies, availability of 64 many ‘omics’ data sets such as metagenomics, transcriptomics and proteomics are some of the factors 65 that have brought microbial interactions to the fore (5-9). Thus, the past few decades have seen a rapid 66 growth in the body of literature on microbial interactions. 67 Bacteria exist in complex multispecies communities which are mostly characterised by competition 68 and to a lesser extent, cooperation (10-12). In these interactions, survival depends on the ability to 69 compete for resources in a given niche. Mechanisms of competition can be either classified as 70 exploitative or interference (10, 13-16). Exploitative competition is passive whereby microbes 71 compete for scarce resources and the winner typically limits nutrient availability from competitors. 72 Interference competition is characterised by production of specialised metabolites. Microbes have a 73 large arsenal of antimicrobial weapons that mediate interference competition and these include 74 contact dependant inhibition (CDI), T6SS, antibiotic and bacteriocin production (17-29). These 75 antimicrobials are diverse in their mechanism of action, targets, antagonistic and spatial range (20, 76 21). There is clearly a cost in the execution of these weapons, hence, by implication, regulation must 77 be tightly modulated (26, 30-32). Over the years, many studies have interrogated mechanisms of the 78 different antimicrobials ‘singularly’ however fewer have systematically investigated these factors in 79 concert. For example a growing number of studies have shown the role, mechanism of action and 80 targets of T6SS, T5SS and bacteriocins in bacterial competitions (22, 28). 81 Soft Rot Enterobacteriaceae (SRE), which were recently reclassified as Soft Rot Pectobacteriaceae 82 (SRP), are a group of pathogens causing huge economic losses on potato production worldwide (33, 83 34). They cause blackleg and soft rot diseases in the field or during post-harvest storage, respectively. 3 bioRxiv preprint doi: https://doi.org/10.1101/497016; this version posted December 17, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 84 Decaying potato tubers are characterised by multispecies bacterial communities that are both Gram 85 positive and negative (7, 33). Furthermore, within the SRE, it is quite normal to isolate bacteria from 86 Pectobacterium spp as well as Dickeya spp, the two primary genera within Pectobacteriaceae from a 87 single infected plant (7). Of these, Pectobacterium carotovorum subsp. brasiliense is an emerging 88 SRE with global distribution (35-40). Previous studies have shown that Pcb strain PBR1692 (referred 89 to hence forth as Pcb1692) is able to inhibit growth of P. carotovorum subsp. carotovorum WPP14 90 (Pcc) and P. atrosepticum SCRI1043 suggesting that many more bacteria can be inhibited by 91 Pcb1692 thus giving it a fitness advantage, in a given ecological niche(41, 42). In this study, we use a 92 combination of metagenomics, in silico analysis and various in vitro and in planta competition assays 93 to identify and characterise bacterial targets, and distinctive roles played by the different antimicrobial 94 produced by Pcb1692, their regulation and possible contribution towards adaptation to diverse 95 ecological niches. 96 97 Results 98 The microbiome of potato tubers 99 A total of 327,032 and 475,616 paired-end reads from diseased and healthy potato, respectively,
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