Quantitative Proteomics Reveals the Temperature-Dependent Proteins Encoded by a Series of Cluster Genes in Thermoanaerobacter Tengcongensis

Abstract

Comprehensive and quantitative information of the thermophile proteome is an important source for understanding of the survival mechanism under high growth temperature. Thermoanaerobacter tengcongensis (T. tengcongensis), a typical anaerobic thermophilic eubacterium, was selected to quantitatively evaluate its protein abundance changes in response to four different temperatures. With optimized procedures of isobaric tags for relative and absolute quantitation quantitative proteomics (iTRAQ), such as peptide fractionation with high-pH reverse phase (RP) high performance liquid chromatography (HPLC), tandem MS acquisition mode in LTQ Orbitrap Velos MS, and evaluation of the quantification algorithms, high quality of the quantitative information of the peptides identified were acquired. In total, 1589 unique proteins were identified and defined 251 as the temperature-dependent proteins. Analysis of genomic locations toward the correspondent genes of these temperature-dependent proteins revealed that more than 30% were contiguous units with relevant biological functions, which are likely to form the operon structures in T. tengcongensis. The RNA sequencing (RNA-seq) data further demonstrated that these cluster genes were cotranscribed, and their mRNA abundance changes responding to temperature exhibited the similar trends as the proteomic results, suggesting that the temperature-dependent proteins are highly associated with the correspondent transcription status. Hence, the operon regulation is likely an energy-efficient mode for T. tengcongensis survival. In addition, evaluation to the functions of differential proteomes indicated that the abundance of the proteins participating in sulfur-respiration on the plasma membrane was decreased as the temperature increased, whereas the glycolysis-related protein abundance was increased.The energy supply in T. tengcongensis at high temperature is, therefore, speculated not mainly through the respiration chain reactions. Molecular & Cellular Proteomics 12: 10.1074/mcp.M112.025817, 2266-2277, 2013.Thermophiles are organisms that live at relatively high temperatures approximately over 50°C or more. Studies on the survival mechanisms of these organisms has drawn great attention, because the relevant knowledge helps us to understand how life can thrive under extreme temperatures, what their potential is in biotechnology, and whether anaerobic thermophiles contain information regarding the early evolutionary life forms on earth. Traditionally, most investigations have focused on the stability of protein structures or enzyme activity. Based on many crystal structures of thermophilic enzymes reported, several factors responsible for their thermo stability have been suggested, such as selected amino acid substitutions (1, 2), hydrophobic cores (3, 4), buried polar contacts and ion pairs (5, 6), as well as interactions among subunits (7,8). On the other hand, it is becoming a realization that even though the thermal-tolerant mechanism for a single protein is completely elucidated, it...

Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H2 and CO2 under different temperature conditions

“…It seems that different microbes use different energy metabolism strategies to cope with temperature stress. Some microorganisms reduce energy metabolism under temperature stress, while others increase it (Chen et al., ; Goodchild et al., ). This finding leads us to hypothesize that M. thermautotrophicus delta H downregulates methane metabolic pathways related to energy production and conversion under conditions of temperature stress, and that inhibitory proteins are synthesized as a survival mechanism following temperature stress.…”

“…iTRAQ labeling and SCX fractionation, LC‐ESI‐MS/MS analysis based on Q EXACTIVE, and data analysis were performed according to the iTRAQ manufacturer's instructions (Chen et al., ; Li et al., ; Liu et al., ; Qiao et al., , ; Tian et al., ).…”

Comparative iTRAQ‐Based Quantitative Proteomic Analysis of Pelteobagrus vachelli Liver under Acute Hypoxia: Implications in Metabolic Responses

“…No significant differences were observed for %CV of ratios between the P4 and P0 group, indicating successful control of outliers in each respective pool . Proteins with a fold change larger than 1.2 and a p ‐value less than 0.05 were considered to be significantly differentially expressed …”

Thermal Stability of Glucokinases inThermoanaerobacter tengcongensis

“…The survival mechanism of such kind of thermophilic bacteria has drawn great attention, due to their potential utilization in industry and elucidation of life evolution. The genome sequencing of T. tengcongensis has been finished in as early as 2002 [2], and its proteome has been surveyed in multiple views [3–6], which makes T. tengcongensis an ideal model for thermophilic mechanism study. …”