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      Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae

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          Abstract

          We present the draft genome sequence of Leptolinea tardivitalis YMTK-2, a member of the Chloroflexi phylum. This organism was initially characterized as a strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates that it encodes for a flagella and might be capable of aerobic respiration.

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          The cytochrome bd respiratory oxygen reductases.

          Vitaliy B. Borisov, Robert B Gennis, James Hemp … (2011)
          Cytochrome bd is a respiratory quinol: O₂ oxidoreductase found in many prokaryotes, including a number of pathogens. The main bioenergetic function of the enzyme is the production of a proton motive force by the vectorial charge transfer of protons. The sequences of cytochromes bd are not homologous to those of the other respiratory oxygen reductases, i.e., the heme-copper oxygen reductases or alternative oxidases (AOX). Generally, cytochromes bd are noteworthy for their high affinity for O₂ and resistance to inhibition by cyanide. In E. coli, for example, cytochrome bd (specifically, cytochrome bd-I) is expressed under O₂-limited conditions. Among the members of the bd-family are the so-called cyanide-insensitive quinol oxidases (CIO) which often have a low content of the eponymous heme d but, instead, have heme b in place of heme d in at least a majority of the enzyme population. However, at this point, no sequence motif has been identified to distinguish cytochrome bd (with a stoichiometric complement of heme d) from an enzyme designated as CIO. Members of the bd-family can be subdivided into those which contain either a long or a short hydrophilic connection between transmembrane helices 6 and 7 in subunit I, designated as the Q-loop. However, it is not clear whether there is a functional consequence of this difference. This review summarizes current knowledge on the physiological functions, genetics, structural and catalytic properties of cytochromes bd. Included in this review are descriptions of the intermediates of the catalytic cycle, the proposed site for the reduction of O₂, evidence for a proton channel connecting this active site to the bacterial cytoplasm, and the molecular mechanism by which a membrane potential is generated. 2011 Elsevier B.V. All rights reserved.
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            Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi.

            Takeshi Yamada, Yuji Sekiguchi, Satoshi Hanada … (2006)
            One thermophilic (strain IMO-1(T)) and two mesophilic (strains KIBI-1(T) and YMTK-2(T)) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class 'Anaerolineae' of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 microm and the width was 0.3-0.4 microm for strain IMO-1(T), 0.4-0.5 microm for strain KIBI-1(T) and thinner than 0.2 microm for strain YMTK-2(T). Strain IMO-1(T) could grow at pH 6.0-7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1(T) was around 50 degrees C (growth occurred between 42 and 55 degrees C). Growth of the mesophilic strains KIBI-1(T) and YMTK-2(T) occurred at pH 6.0-7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25-50 degrees C with optimal growth at around 37 degrees C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G + C contents of the DNA of strains IMO-1(T), KIBI-1(T) and YMTK-2(T) were respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1(T) were anteiso-C(17 : 0), iso-C(15 : 0), C(16 : 0) and anteiso-C(15 : 0), whereas those for mesophilic strains KIBI-1(T) and YMTK-2(T) were branched C(14 : 0), iso-C(15 : 0), C(16 : 0) and branched C(17 : 0), and branched C(17 : 0), C(16 : 0), C(14 : 0) and C(17 : 0), respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon 'Anaerolineae' of the bacterial phylum Chloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylum Chloroflexi. Here, Anaerolinea thermolimosa sp. nov. (type strain IMO-1(T) = CM 12577(T) = DSM 16554(T)), Levilinea saccharolytica gen. nov., sp. nov. (type strain KIBI-1(T) = JCM 12578(T) = DSM 16555(T)) and Leptolinea tardivitalis gen. nov., sp. nov. (type strain YMTK-2(T) = JCM 12579(T) = DSM 16556(T)) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon 'Anaerolineae' into Anaerolineae classis nov. and Caldilineae classis nov. We also propose the subordinate taxa Anaerolineales ord. nov., Caldilineales ord. nov., Anaerolineaceae fam. nov. and Caldilineaceae fam. nov.
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              Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war.

              Iain C. Sutcliffe (2011)
              It is important that attempts to understand bacterial phylogeny take into account fundamental bacterial characteristics such as cell envelope composition and organization. Several prominent phylogenetic studies have assumed that the cell envelopes of members of the phylum Chloroflexi are 'gram-negative' (diderm, i.e. defined by both an inner plasma membrane and an outer membrane) and some of these studies have placed the branch leading to the extant Chloroflexi near the root of the bacterial phylogenetic tree. This Correspondence summarizes the compelling evidence that the Chloroflexi are in fact monoderm, i.e. have only a single cellular membrane. The phylogenetic implications of this conclusion are discussed. The data reviewed also shed interesting light on the distribution of protein secretion systems in diderm bacteria.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 19 November 2015
                Publication date Collection: Nov-Dec 2015
                Volume: 3
                Issue: 6
                Electronic Location Identifier: e01356-15
                Affiliations
                [a ]Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
                [b ]Department of Medicine, University of California San Diego, La Jolla, California, USA
                Author notes
                Address correspondence to James Hemp, jimhemp@ 123456caltech.edu .
                Article
                Publisher ID: genomeA01356-15
                DOI: 10.1128/genomeA.01356-15
                PMC ID: 4653795
                PubMed ID: 26586893
                SO-VID: 3b415e11-da61-4f76-88b4-5a48efdd09b6
                Copyright © Copyright © 2015 Ward et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 29 September 2015
                Date accepted : 5 October 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 6, Pages: 1, Words: 838
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date November/December 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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