scholarly journals Edaphic controls on genome size and GC content of bacteria in soil microbial communities

2021 ◽  
Author(s):  
Peter Francis Chuckran ◽  
Cody Flagg ◽  
Jeffrey Propster ◽  
William Austin Rutherford ◽  
Ella T. Sieradzki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Genome Size ◽  
Acid Content ◽  
Bacterial Genome ◽  
Soil Microbial Communities ◽  
Gc Content ◽  
Amino Acid Content ◽  
The United States ◽  
Soil Bacterial

Genomic traits, such as genome size, GC content, codon usage, and amino acid content, shed insight into the evolutionary processes of bacteria and selective forces behind microbial community composition. Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition, yet little research has been conducted in the soil environment, and the factors which shape soil bacterial genomic traits remain largely unknown. Here we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across the United States from the National Ecological Observation Network (NEON) and observed the distribution of these traits across numerous environmental gradients. We found that genomic trait averages were most strongly related to pH, which we suggest results in both physiological constraints on growth as well as affects availability of nutrients in soil. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with larger genomes and lower GC-content, potentially a result of increased physiological stress and increased metabolic diversity. Conversely, smaller genomes with high GC content were associated with high pH and low soil carbon to nitrogen ratios, indicating potential resource driven selection against carbon-rich AT base pairs. We found that this relationship of nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms which underpin nucleotide and amino acid selection in soil bacterial communities.

Development of high protein soybean experimental lines with enhanced sulfur amino acid content

2019 ◽  
Author(s):  
◽  
Alaa Alaswad
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Nutritive Value ◽  
Animal Feed ◽  
Amino Acid Content ◽  
The United States ◽  
High Protein ◽  
Sulfur Amino Acid ◽  
Soybean Line ◽  
Modest Improvement

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Soybean is one of the most important field crops grown in the United States. Commercial soybeans contain about 36 - 40% protein and 18 - 20% oil, by dry weight. Most of the soybean produced in the U.S. is utilized for oil production and animal feed. Even though soybean is a rich source of protein for livestock and humans, the nutritional quality of soybean can be further enhanced if the concentration of sulfur containing amino acids, methionine and cysteine, can be increased. Previously, our lab has employed transgenic approaches to increase the nutritive value of soybean by expressing heterologous sulfur-rich seed proteins and by manipulating the sulfur assimilatory pathway. Even though modest improvement in the nutritive value has been obtained by these approaches, till now no high yielding soybean cultivars with high protein and high sulfur amino acid content has been developed. Such cultivars will be of great value for the agricultural industry especially in animal feed. In this study, I have crossed a South Korean high protein soybean line (Lee5) with a transgenic soybean line with elevated sulfur amino acid content (CS) and developed soybean experimental lines that were advanced to F4:5 seeds. Theses experimental lines exhibit both high protein and high sulfur amino acid content. The protein content of their seeds has been increased 8 to 14% while their oil content has decreased 5 to 7% when compared with CS. Furthermore, I have successfully introduced the cytosolic isoform of O-acetylserine sulfhydrylase (OASS), the overexpressed transgene, from CS into these crosses. The activity of OASS has been increased 5 to 20-fold in experimental lines when compared to Lee5.

scholarly journals Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate Symbiont Buchnera aphidicola

2005 ◽  
Vol 187 (12) ◽  
pp. 4229-4237 ◽  
Author(s):  
Nancy A. Moran ◽  
Helen E. Dunbar ◽  
Jennifer L. Wilcox
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Acyrthosiphon Pisum ◽  
Bacterial Genome ◽  
Amino Acid Content ◽  
Transcript Abundance ◽  
Regulation Of Transcription ◽  
Buchnera Aphidicola ◽  
Obligate Symbiont ◽  
Dietary Amino Acid

ABSTRACT Buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays for B. aphidicola of the host Schizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response was metE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host, Acyrthosiphon pisum, B. aphidicola has no functional metR and shows no response in metE transcript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.

scholarly journals Kullback Leibler divergence in complete bacterial and phage genomes

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4026
Author(s):  
Sajia Akhter ◽  
Ramy K. Aziz ◽  
Mona T. Kashef ◽  
Eslam S. Ibrahim ◽  
Barbara Bailey ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Gc Content ◽  
Amino Acid Content ◽  
Large Set ◽  
Metagenomic Sequence ◽  
Amino Acid Utilization ◽  
A Genome ◽  
Leibler Divergence ◽  
Significant Difference

The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback–Leibler divergence from the mean amino acid content as a metric to compare the amino acid composition for a large set of bacterial and phage genome sequences. Using these data, we demonstrate that (i) there is a significant difference between amino acid utilization in different phylogenetic groups of bacteria and phages; (ii) many of the bacteria with the most skewed amino acid utilization profiles, or the bacteria that host phages with the most skewed profiles, are endosymbionts or parasites; (iii) the skews in the distribution are not restricted to certain metabolic processes but are common across all bacterial genomic subsystems; (iv) amino acid utilization profiles strongly correlate with GC content in bacterial genomes but very weakly correlate with the G+C percent in phage genomes. These findings might be exploited to distinguish coding from non-coding sequences in large data sets, such as metagenomic sequence libraries, to help in prioritizing subsequent analyses.

scholarly journals The effects of insulin and adrenaline on the amino-acid content of blood

1933 ◽  
Vol 27 (5) ◽  
pp. 1648-1654 ◽  
Author(s):  
James Murray Luck ◽  
Stanley Wallace Morse
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Amino Acid Content
Sign in / Sign up

Export Citation Format

Share Document