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Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

View Article: PubMed Central - PubMed

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Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

No MeSH data available.


Proportional Venn diagram depicting the shared and unique gene fractions between HIMB624, HTCC2181, and two closely related strains from within the family Methylophilaceae, Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4.
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f4: Proportional Venn diagram depicting the shared and unique gene fractions between HIMB624, HTCC2181, and two closely related strains from within the family Methylophilaceae, Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4.

Mentions: Of 1,381 protein encoding genes in the genome of HIMB624, 1,135 are shared with HTCC2181, representing 82-84% of the two genomes (Figure 4). Pathways for the synthesis of all twenty amino acids are present in both strains, as well as for the synthesis of all major vitamins except B12. The family Methylophilaceae consists of obligate methylotrophs and, while HIMB624 and HTCC2181 lack genes coding for either the large (mxaF) or small (mxaI) subunit of a confirmed methanol dehydrogenase, both organisms appear to have genes coding for a related analog of mxaF, known as xoxF. Methanol dehydrogenase activity of this paralog has been questioned for some time (see [4] and references therein), but current evidence suggests that the xoxF genes in these organisms code for a large subunit having methanol dehydrogenase activity [4]. The xoxF gene in HIMB624 is 87.4% similar in protein sequence to the xoxF gene in HTCC2181. Strains HTCC2181 and HIMB624 also have many of the other subunits required to form a methanol dehydrogenase holoenzyme including mxaA,C,D,E,G,J,K,R,L and S, and operons pqqBCDEFG. Neither strain possesses genes coding for the E1 subunit (sucA, EC:1.2.4.2) of the α-ketoglutarate dehydrogenase complex, though they do appear to possess the E2 subunit (sucB, EC: 2.3.1.61). Both subunits are required to complete the tricarboxylic acid (TCA) cycle, and the absence of the E1 subunit suggests that these strains are obligate methylotrophs.


Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

Proportional Venn diagram depicting the shared and unique gene fractions between HIMB624, HTCC2181, and two closely related strains from within the family Methylophilaceae, Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368401&req=5

f4: Proportional Venn diagram depicting the shared and unique gene fractions between HIMB624, HTCC2181, and two closely related strains from within the family Methylophilaceae, Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4.
Mentions: Of 1,381 protein encoding genes in the genome of HIMB624, 1,135 are shared with HTCC2181, representing 82-84% of the two genomes (Figure 4). Pathways for the synthesis of all twenty amino acids are present in both strains, as well as for the synthesis of all major vitamins except B12. The family Methylophilaceae consists of obligate methylotrophs and, while HIMB624 and HTCC2181 lack genes coding for either the large (mxaF) or small (mxaI) subunit of a confirmed methanol dehydrogenase, both organisms appear to have genes coding for a related analog of mxaF, known as xoxF. Methanol dehydrogenase activity of this paralog has been questioned for some time (see [4] and references therein), but current evidence suggests that the xoxF genes in these organisms code for a large subunit having methanol dehydrogenase activity [4]. The xoxF gene in HIMB624 is 87.4% similar in protein sequence to the xoxF gene in HTCC2181. Strains HTCC2181 and HIMB624 also have many of the other subunits required to form a methanol dehydrogenase holoenzyme including mxaA,C,D,E,G,J,K,R,L and S, and operons pqqBCDEFG. Neither strain possesses genes coding for the E1 subunit (sucA, EC:1.2.4.2) of the α-ketoglutarate dehydrogenase complex, though they do appear to possess the E2 subunit (sucB, EC: 2.3.1.61). Both subunits are required to complete the tricarboxylic acid (TCA) cycle, and the absence of the E1 subunit suggests that these strains are obligate methylotrophs.

View Article: PubMed Central - PubMed

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

No MeSH data available.