DOCSLIB.ORG

I – Microbial Ecology – Smb2101

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
I – Microbial Ecology – Smb2101 SCHOOL OF BIO AND CHEMICAL ENGINEERING DEPARTMENT OF BIOTECHNOLOGY UNIT – I – MICROBIAL ECOLOGY – SMB2101 1 UNIT:1 MICROBIAL HABITATS Microbial ecology or environmental microbiology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life— Eukaryota, Archaea, and Bacteria—as well as viruses. Microbial Habitats • Microbes are present in every kind of habitat. • Microbes are incredibly diverse thriving in environments from the very cold to the extremely hot. • They are also tolerant of many other conditions such as limited water availability, high salt content and low oxygen levels. • Not every microbe can survive in all habitats. Terrestrial Microbial Habitats: Microbes lives in/on soil. • Only one percent of microbes that live in soil have been identified. • These organisms take part in the formation of soil and are essential components of their ecosystems. • Bacteria and fungi that live in soil feed mostly on organic matter such as other plants and animals. • These microbes are very sensitive to their local environment. • Factors such as the levels of carbon dioxide, oxygen, pH, moisture and temperature all affect the growth of microbes in the soil. Microbial Habitats in Other Organisms • Microbes also live on other organisms. • As with the ones found on people these microbes can be harmful or beneficial to the host. Example: 2 • Bacteria grow in nodules on the roots of pea and bean plants. • These microbes convert nitrogen from the air into a form that the plants can use. • In many ways animals and plants have evolved as habitats for the millions of microbes that call them home. Extreme Microbial Environments • The microbes living in extreme conditions are called extremophiles. • This literally means that they love the extreme conditions of their habitat. • The extremophiles are so well adapted to their own environment. • Some like the ones in hot springs need extreme temperatures to grow. ROLE OF MICROBES IN BIOGEOCHEMICAL CYCLE Nutrients move through the ecosystem in biogeochemical cycles. • A biogeochemical cycle is a pathway by which a chemical element (such as carbon or nitrogen) circulates through the biotic (living) and the abiotic (non-living) factors of an ecosystem. • The elements that move through the factors of an ecosystem are not lost but are instead recycled or accumulated in places called reservoirs (or “sinks”) where they can be held for a long period of time. • Elements, chemical compounds, and other forms of matter are passed from one organism to another and from one part of the biosphere to another through these biogeochemical cycles. • Microorganisms play a primary role in regulating biogeochemical systems in virtually all of our planet’s environments. This includes extreme environments such as acid lakes and hydrothermal vents, and even includes living systems such as the human gut. • The key collective metabolic processes of microbes (including nitrogen fixation, carbon fixation, methane metabolism, and sulfur metabolism) effectively control global biogeochemical cycling. 3 • Incredibly, production by microbes is so immense that global biogeochemistry would likely not change even if eukaryotic life were totally absent! • Microbes comprise the backbone of every ecological system, particularly those in which there is no light (i.e. systems in which energy cannot be collected through photosynthesis ) MICROBIAL SUCESSION • Ecological succession is the process of change in the species structure of an ecological community over time. The time scale can be decades (for example, after a wildfire), or even millions of years after a mass extinction • Succession of micro-organisms including fungi and bacteria occurring within a microhabitat is known as microsuccession or serule. • Like in plants, microbial succession can occur in newly available habitats (primary succession) such as surfaces of plant leaves, recently exposed rock surfaces (i.e., glacial till) or animal infant guts, • Growth on disturbed communities (secondary succession) like those growing in recently dead trees or animal droppings. • Microbial communities may also change due to products secreted by the bacteria present. Changes of pH in a habitat could provide ideal conditions for a new species to inhabit the area. Membrane biofouling in waste water reactor: An example for microbial succession • In Phase I (0–2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar extracellular polymeric substances (EPS) and microbial community composition as the early biofilms. • Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. 4 • In Phase II (2–4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). • The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. • In Phase III (5–14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. • The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling • In some cases the new species may outcompete the present ones for nutrients leading to the primary species demise. Changes can also occur by microbial succession with variations in water availability and temperature. SOIL MICROFLORA • Microflora means, bacteria and microscopic algae and fungi, living in a particular site or habitat. • 1 g of soil contain • 100,000,000 bacterial cells • 11,000 species of bacteria • Also fungi and larger animals Types of Microbes in Soil • Prokaryotic Bacteria, Actinomycetes • Fungi • Algae • Protozoa • Viruses 5 BACTERIA • Tiny 1µm width, one celled • Single cell division • 1can produce 5 billion in 12 hours in lab • (in environment limited by predators, water and food availability) • Abundant in rhizosphere • Zone surrounding root –dead root cells and exudate stimulate microbial growth MAIN TYPES OF SOIL BACTERIA • Agarobacterium, Alcaligenes • igenes, Bacillus • Arthrobacter, Cellulomonas Corynebacterium • Caulobacter, Micrococcus • Clostridum, Pseudomonas • Flavobacterium, Achromobacter • Methanobacterium • Chromobacterium • Agarobacterium, Alcaligenes • igenes, Bacillus • Arthrobacter, Cellulomonas Corynebacterium • Caulobacter, Micrococcus • Clostridum, Pseudomonas • Flavobacterium, Achromobacter 6 • Methanobacterium • Chromobacterium SOIL BACTERIA-ROLE IN SOIL • Degrade organic matter • Fix N2-and other steps of N cycle • Rhizobium-nitrogen fixation • Nitrification-Nitrosomonas, Nitrobacter • Organisms involved with vital functions may be in lower aboundance • Organisms present will depend on many factors-Nutrients, O2, Moisture, pH. SOIL ACTIOMYCETES • Degrade organic matter • Fix N2-and other steps of N cycle • Rhizobium-nitrogen fixation • Nitrification-Nitrosomonas, Nitrobacter • Organisms involved with vital functions may be in lower aboundance • Organisms present will depend on many factors-Nutrients, O2, Moisture, pH. • Actinomycetes are slow growing compared to bacteria and fungi • Streptomyces may be up to 65% of soil population • Nocardia and Micromonospora upto 35% of population • Other common genera • Streptosporangium • Actinoplanes • Thermoactinomyces 7 • Thermomonospora • Role of Actinomycetes in soil1. Organic matter decomposition • Starch, cellulose, hemicellulose, lignin, humus 2. Antibiotic production • Streptomycin, tetracycline, chloramphenicol • 3. Maintain Microbial equillibrium in soil • Control pathogenic organisms • Produce proteases lyse cells of pathogens • Fungi Grow as long threads (hyphe) • Push through soil particles, roots, rocks • Often group into masses called mycelium (look like roots) • Higher fungi have basidium: club shaped structure • Bearing fruiting body PREDOMINANT FUNGI IN SOILFUNGI IMPERFECTI: MOST PREDOMINANT GROUP IN SOIL • Cephalosporium • Verticillium • Monilia • Trichoderma • Fusarium • Cladosporium • Gliocladium • Role of fungi in soil Organic matter degradation: Degrade starch, hemicellulose, cellulose, lignin, • Ammonification: degrade proteins, nucleicacids and release NH3 8 • Control of other organisms: some fungi kill nematodes • Pathogenicity: Many fungi associated with plant disease-ythium, Sclerotinia, Puccinia • Formation of mycorrhizae, symbiotic relationship with plant root. • AlgaeFilamentous, colonial, unicellular • Photsynthetic • Most in blue –green group, but also yellow-green, diatoms, green algae • Form carbonic acid (weathering) • Add OM(Organic matter) to soil, bind particles • Aeration • Some fix nitrogen • Algal groups in soilChlorophyaceae-Green algae • Cyabophyaceae-Bluegreen algae • Bacillariophyaceae: Diatoms • Xanthophyaceae-Yellow green algae • Importance of algae in soilProvide organic matter • Many algae produce polysaccharides, improve soil structure • Produce oxygen, provide oxygen to rice plants • Fix nitrogen and provide to rice plants after decomptosition STRATIFICATION OF FRESHWATER • Freshwater are areas which having low salt concentration approximately less than 1%, and organisms that can not survive in other regions that have high salt concentration such as sea and oceans. 9 Types 1. Ponds and
Load more

Recommended publications
  • Review Pili in Gram-Negative and Gram-Positive Bacteria – Structure
    Cell. Mol. Life Sci. 66 (2009) 613 – 635 1420-682X/09/040613-23 Cellular and Molecular Life Sciences DOI 10.1007/s00018-008-8477-4 Birkhuser Verlag, Basel, 2008 Review Pili in Gram-negative and Gram-positive bacteria – structure, assembly and their role in disease T. Profta,c,* and E. N. Bakerb,c a School of Medical Sciences, Department of Molecular Medicine & Pathology, University of Auckland, Private Bag 92019, Auckland 1142 (New Zealand), Fax: +64-9-373-7492, e-mail: [email protected] b School of Biological Sciences, University of Auckland, Auckland (New Zealand) c Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland (New Zealand) Received 08 August 2008; received after revision 24 September 2008; accepted 01 October 2008 Online First 27 October 2008 Abstract. Many bacterial species possess long fila- special form of bacterial cell movement, known as mentous structures known as pili or fimbriae extend- twitching motility. In contrast, the more recently ing from their surfaces. Despite the diversity in pilus discovered pili in Gram-positive bacteria are formed structure and biogenesis, pili in Gram-negative bac- by covalent polymerization of pilin subunits in a teria are typically formed by non-covalent homopo- process that requires a dedicated sortase enzyme. lymerization of major pilus subunit proteins (pilins), Minor pilins are added to the fiber and play a major which generates the pilus shaft. Additional pilins may role in host cell colonization. be added to the fiber and often function as host cell This review gives an overview of the structure, adhesins. Some pili are also involved in biofilm assembly and function of the best-characterized pili formation, phage transduction, DNA uptake and a of both Gram-negative and Gram-positive bacteria.
    [Show full text]
  • Infection at the Wildlife-Livestock-Human Interface: Three Systems
    Infection at the Wildlife- livestock-human interface: three systems Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Elsa Sandoval Barron 12/4/2017 Abstract Zoonoses involve interactions between at least three species: the pathogen and two hosts, one of which is human and the other a non-human (vertebrate) animal. More than 60% of human infectious diseases are zoonotic, and many have a wildlife host. Urbanisation and human population growth have increased the demand for food and land resources, which have increased interaction between humans, domestic animals and wildlife and thus the potential for cross-species transmission of infections. Most studies of such systems take place in tropical and developing countries where population change and biodiversity makes the emergence of high profile infections (eg Ebola and SARS) more likely. This study, however, focuses on four well known infections within the UK: bovine tuberculosis, water-borne cryptosporidiosis and giardiasis, and campylobacteriosis. The aim of this study was to investigate, using four infectious diseases of economic and public health importance in the UK as study systems, the role of wildlife in the epidemiology of multihost, zoonotic infections. Bovine tuberculosis (bTB) is an important zoonosis in many parts of the world, but human infection is rare in the UK owing to a policy of ‘test and cull’ in cattle and pasteurisation of milk. However, there has been an epidemic of bTB in British cattle in recent decades, the control of which is complicated by infection in badgers (Meles meles) and controversy over the control of wildlife infection.
    [Show full text]
  • MYCOBACTERIA.Pdf
    MYCOBACTERIA Mycobacteria are widespread organisms, typically living in and food sources. Tuberculosis and the leprosy organisms are obligate parasites and are not found as free-living members of the genus. Mycobacteria are aerobic and nonmotile bacteria (except for the species Mycobacterium marinum, which has been shown to be motile within macrophages) that are characteristically acid fast. Mycobacteria have an outer membrane. They do not have capsules, and most do not form endospores. The distinguishing characteristic of all Mycobacterium species is that the cell wall is thicker than in many other bacteria, which is hydrophobic, waxy, and rich in mycolic acids/mycolates. The cell wall consists of the hydrophobic mycolate layer and a peptidoglycan layer held together by a polysaccharide, arabinogalactan. The cell wall makes a substantial contribution to the hardiness of this genus. The biosynthetic pathways of cell wall components are potential targets for new drugs for tuberculosis. Fig. 1 Mycobacterial cell wall: 1-outer lipids, 2-mycolic acid, 3-polysaccharides (arabinogalactan), 4-peptidoglycan, 5-plasma membrane, 6-lipoarabinomannan (LAM), 7- phosphatidylinositol mannoside, 8-cell wall skeleton. NONTUBERCULOUS MYCOBACTERIA – RUNYON CLASSIFICATION Runyon classification is a system of identifying mycobacteria on the basis of pigmentation and growth condition of the organisms. The Runyon classification of nontuberculous mycobacteria based on the rate of growth, production of yellow pigment and whether this pigment was produced in the dark or only after exposure to light. It was introduced by Ernest Runyon in 1959 (Fig. 111). On these bases, the nontuberculous mycobacteria are divided into four groups: Photochromogens (Group I) - produce nonpigmented colonies when grown in the dark and pigmented colonies only after exposure to light and reincubation (1M.
    [Show full text]
  • Streptococcus Pneumoniae Capsular Polysaccharide Is Linked to Peptidoglycan Via a Direct Glycosidic Bond to Β-D-N-Acetylglucosamine
    Streptococcus pneumoniae capsular polysaccharide is linked to peptidoglycan via a direct glycosidic bond to β-D-N-acetylglucosamine Thomas R. Larsona and Janet Yothera,1 aDepartment of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170 Edited by Emil C. Gotschlich, The Rockefeller University, New York, NY, and approved April 14, 2017 (received for review December 20, 2016) For many bacteria, including those important in pathogenesis, (Und-P). In S. pneumoniae serotype 2 CPS, Glcp-1-P is trans- expression of a surface-localized capsular polysaccharide (CPS) can ferred from UDP-Glcp (11), and this is followed by addition of be critical for survival in host environments. In Gram-positive the remaining sugars (12, 13) to form the complete repeat unit bacteria, CPS linkage is to either the cytoplasmic membrane or the (Fig. 1). Und-P-P-oligosaccharide repeat units are translocated cell wall. Despite the frequent occurrence and essentiality of these to the outer face of the cytoplasmic membrane by Wzx and po- polymers, the exact nature of the cell wall linkage has not been lymerized into high molecular weight (MW) polysaccharide by described in any bacterial species. Using the Streptococcus pneu- Wzy. Growth occurs at the reducing end, with single or multiple moniae serotype 2 CPS, which is synthesized by the widespread repeat units being transferred en bloc from Und-P-P to an ac- Wzy mechanism, we found that linkage occurs via the reducing ceptor Und-P-P-oligosaccharide repeat unit. Hydrolysis of the β N- end glucose of CPS and the -D- acetylglucosamine (GlcNAc) res- donor Und-P-P that remains after transfer yields Und-P, which is idues of peptidoglycan (PG).
    [Show full text]
  • Engineering the Human Microbiome, a Natural Double-Barreled Approach Towards Solving Both Our Current Antibiotic Resistance and Sepsis Problems
    American Journal of www.biomedgrid.com Biomedical Science & Research ISSN: 2642-1747 --------------------------------------------------------------------------------------------------------------------------------- Opinion Copy Right@ Toleman MA Engineering the Human Microbiome, A Natural Double-Barreled Approach Towards Solving both our Current Antibiotic Resistance and Sepsis Problems Martins W1, Mathias J1, Babenko D2 and Toleman MA1* 1Cardiff University Medical school, Department of Immunology and Infection, The Heath hospital, UK 2Karaganda Medical University, Kazakhstan *Corresponding author: Toleman MA, Cardiff University Medical school, Department of Immunology and Infection, The Heath hospital, Cardiff, UK. To Cite This Article: Martins W, Mathias J, Babenko D, Toleman MA, Engineering the Human Microbiome, A Natural Double-Barreled Approach Towards Solving both our Current Antibiotic Resistance and Sepsis Problems. Am J Biomed Sci & Res. 2020 - 11(3). AJBSR.MS.ID.001632. DOI: 10.34297/AJBSR.2020.11.001632. Received: December 12, 2020; Published: December 18, 2020 Opinion resistance mechanism responsible for this rise was an enzyme Many of the bacteria that cause life-threatening infection live called CTX-M-15 that gave resistance to the penicillin, monobactam, in very close association with us. Escherichia coli, for example and cephalosporin classes of the ß-lactam family of antibiotics (c. causes 80% of common community associated urinary tract infections and is also the main cause of serious (blood-stream) in several enteric pathogens including E. coli in New Delhi, India infection throughout Europe [1,2]. However, E. coli routinely lives 50% of all antibiotics) [7]. Its gene blaCTX-M-15 was first isolated in 2000 [8]. Later publications indicated that it was widespread as a commensal organism in our gut.
    [Show full text]
  • Current Issues of Nano-Bio-Science
    Current Issues of Nano-Bio-Science CeNS Winterschool 2003 Mauterndorf, Austria 24-28 February 2003 Current Issues of Nano-Bio-Science CeNS Winterschool 2003 Mauterndorf, Austria 24-28 February 2003 in cooperation with SFB 486 and SFB 513 Program Committee Organisation Christoph Bräuchle Monika Kaempfe Jan von Delft Evelyn Morgenroth Hermann Gaub Joachim Rädler Jörg P. Kotthaus Paul Leiderer Joachim Rädler Internal Students’ Seminar: Schedule Saturday, 22nd February 7:30 pm Meeting in front of the castle’s lower gate to go the “Skialm” together 8:00 pm Get-together at the „Skialm“ in Mauterndorf (in the Skiing center) (kitchen closes at 9:30 pm) Sunday, 23rd February 9:45 am Introduction (W. Parak, F. Simmel) 10:00 am Simon Keller (AG Rädler) 10:30 am Stefan Griessl (AG Heckl) 11:00 am Coffee break 11:30 am Christine Meyer (AG Kotthaus) 12:00 pm Michael Sindel (AG von Delft) 12:30 pm Lunch (not provided), informal discussions 5:00 pm Ferdinand Kühner (AG Gaub) 5:30 pm Stefan Beyer (NG Simmel) Teresa Pellegrino (NG Parak) 6:00 pm Stefan Kowarik (AG Feldmann) 6:30 pm Break 7:00 pm Niklolay Petkov (AG Bein) 7:30 pm Sebastian Gritschneder (AG Reichling) 8:00 pm Ralf Bausinger / Johanna Kirstein (AG Bräuchle) 8:30 pm Conclusion Program Monday, 24th February 2003 8.30 – 8.45 Opening 8.45 – 9.45 Cees Dekker, Delft University of Technology Carbon nanotubes as model systems for nanoelectronics and nanosensors 9.45 – 10.45 Ulf Diederichsen, Universität Göttingen Molecular architecture with biooligomers 10.45 – 11.15 Coffee Break 11.15 – 12.15 Wolfgang
    [Show full text]
  • Cell Structure and Function in the Bacteria and Archaea
    4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth.
    [Show full text]
  • Chemical Probes to Visualize Bacterial Cell Structure and Physiology
    molecules Review From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology Jonathan Hira 1, Md. Jalal Uddin 1 , Marius M. Haugland 2 and Christian S. Lentz 1,* 1 Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; [email protected] (J.H.); [email protected] (M.J.U.) 2 Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; [email protected] * Correspondence: [email protected] Academic Editor: Steven Verhelst Received: 30 September 2020; Accepted: 23 October 2020; Published: 26 October 2020 Abstract: Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways. Keywords: activity-based probe; antibiotic conjugate; bacterial imaging; bacterial uptake; fluorogenic substrate; metabolic labeling; phenotypic heterogeneity 1. Introduction—From 19th Century Microbiology to Modern Day Chemical Biology If chemical biology can be defined as the ‘interrogation of biological systems with chemical approaches’ [1], we must acknowledge some of the first microbiologists as chemical biologists.
    [Show full text]
  • Emerging Frontiers in Microbiome Engineering.Pdf
    Trends in Immunology Review Emerging Frontiers in Microbiome Engineering Marı´a Eugenia Inda,1,2,5 Esther Broset,3,4,5 Timothy K. Lu,1,2,* and Cesar de la Fuente-Nunez3,* The gut microbiome has a significant impact on health and disease and can actively contribute to Highlights obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disor- Themicrobiomeplaysafunda- ders. We do not yet have the necessary tools to fine-tune the microbial communities that consti- mental role in our health and tute the microbiome, though such tools could unlock extensive benefits to human health. Here, disease. we provide an overview of the current state of technological tools that may be used for micro- biome engineering. These tools can enable investigators to define the parameters of a healthy Engineering the microbiome might enable studying the contribution of microbiome and to determine how gut bacteria may contribute to the etiology of a variety of individual microbes and generating diseases. These tools may also allow us to explore the exciting prospect of developing targeted potential therapies against meta- therapies and personalized treatments for microbiome-linked diseases. bolic (e.g., phenylketonuria and chronic kidney disease), inflamma- tory, and immunological diseases, Modulating the Microbiome: An Emerging Paradigm for Understanding and Treating among others. Human Diseases Current methods for probing the The human body is home to at least as many microbial cells as human cells [1]. However, the most microbiome include fecal micro- salient characteristic of the interaction between microbes and the human body is not the number biota transplantation and the use of of cells involved, but their inextricable link with each other.
    [Show full text]
  • Multiple Conformations Facilitate Pilt Function in the Type IV Pilus
    bioRxiv preprint doi: https://doi.org/10.1101/672212; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Multiple conformations facilitate PilT function in the type IV pilus Matthew McCallum1,2, Samir Benlekbir2, Sheryl Nguyen2, Stephanie Tammam2, John L. Rubinstein1,2,3,*, Lori L. Burrows4,*, and P. Lynne Howell1,2,* 1Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada 2Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for SicK Children, Toronto, ON M5G 0A4, Canada. 3Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1l7, Canada. 4Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada. To whom correspondence should be addressed: Dr. Lynne Howell. Phone: 416-813-5378; Email: [email protected] Dr. Lori Burrows, Phone: 905-525-9140, x22029; Email: [email protected] Dr. John Rubinstein. Phone 416-813-7255; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/672212; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Type IV pilus-like systems are protein complexes that polymerize a fibre of pilins. They are critical for virulence in many pathogens. Pilin polymerization and depolymerization are powered by motor PilT-like ATPases thought to possess C2 symmetry. However, most PilT-like ATPases crystallize with either C3 or C6 symmetry and the relevance of these conformations is unclear.
    [Show full text]
  • Arrayed Crispri and Quantitative Imaging Describe the Morphotypic Landscape of Essential Mycobacterial Genes
    RESEARCH ARTICLE Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes Timothy J de Wet1,2*, Kristy R Winkler1,2, Musa Mhlanga2,3, Valerie Mizrahi1,2,4, Digby F Warner1,2,4* 1SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town, Cape Town, South Africa; 2Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; 3Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; 4Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa Abstract Mycobacterium tuberculosis possesses a large number of genes of unknown or predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular chromosomal localizations in the related non-pathogen, M. smegmatis. Applying automated imaging and analysis to 263 essential gene knockdown mutants in an arrayed library, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to inform investigations of gene function. Exploiting this observation, we infer the existence of a mycobacterial restriction- modification system, and identify filamentation as a defining mycobacterial response to histidine *For correspondence: [email protected] (TJW); starvation. Our results support the application of large-scale image-based analyses for [email protected] (DFW) mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.
    [Show full text]
  • Mycolic Acid (M4537)
    Mycolic acid from Mycobacterium tuberculosis (bovine strain) Catalog Number M4537 Storage Temperature –20 °C CAS RN 37281-34-8 Due to the high lipid content of the cell wall, mycobacteria do not stain well with Gram stain Product Description techniques. Heat and a solvent such as phenol are Among different groups of bacteria (e.g., Gram-positive, required for stains to penetrate mycobacteria. Once Gram-negative, spirochetes, mycobacteria, and stained, however, the bacteria retain the stain even mycoplasma), there are various types of cell envelopes when flooded with mineral acids and alcohols. This that represent a departure from the normal simplicity of ability to retain stains after acid washings defines bacterial cell structure compared to animal cells. acid-fast bacteria. Included among the components of the mycobacterium The impermeable cell wall impedes the entry of cell envelope are the cytoplasmic membrane, the cell nutrients causing mycobacteria to grow slowly, but the wall, and the capsule. The cytoplasmic membrane is a low permeability also contributes to the organism’s high phospholipid bilayer unit membrane similar to that resistance to chemical agents and resistance to found in eukaryotic cells. Overlaying the cytoplasmic lysosomal digestion by phagocytes. membrane is a structure consisting of a number of polymers called the cell wall. As for most types of Successful lysis of Mycobacterium tuberculosis by bacteria, highly crosslinked peptidoglycan is a phagocytes causes the release of mycolic acid. The component of the cell wall. Surrounding the cell wall is mycolic acid molecules bind to receptors on an outer layer called the capsule consisting of macrophages causing them to release cytokines such polysaccharide and protein with traces of lipid.1 as tumor necrosis factor-alpha (TNF-a).
    [Show full text]