Clinical practice guidelines for molecular tumor marker, 2nd edition review part 2

In recent years, rapid advancement in gene/protein analysis technology has resulted in target molecule identification that may be useful in cancer treatment. Therefore, "Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition" was published in Japan in September 2021. These guidelines were established to align the clinical usefulness of external diagnostic products with the evaluation criteria of the Pharmaceuticals and Medical Devices Agency. The guidelines were scoped for each tumor, and a clinical questionnaire was developed based on a serious clinical problem. This guideline was based on a careful review of the evidence obtained through a literature search, and recommendations were identified following the recommended grades of the Medical Information Network Distribution Services (Minds). Therefore, this guideline can be a tool for cancer treatment in clinical practice. We have already reported the review portion of "Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition" as Part 1. Here, we present the English version of each part of the Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition.

Difference in immunohistochemical findings among anti-PD-L1 antibodies and their relationships with CD4+ and CD8+ T cells in Japanese melanoma patients

BACKGROUND

The immunohistochemical evaluation of programmed death ligand 1 (PD-L1) is important for selecting treatments. Several antibodies are available for such evaluations, but data regarding the differences in the antibodies' positivity are limited in melanoma, particularly the acral and mucosal types. We investigated the differences in melanoma tissues' PD-L1 expression among the commonly used PD-L1 antibodies and then evaluated the relationship between PD-L1+ tumor cells and tumor-infiltrating lymphocytes (TILs).

PATIENTS AND METHODS

We examined 56 primary lesions and 8 metastatic lymph node samples from 56 Japanese patients with melanoma (28 acral melanoma, 8 mucosal melanoma, 18 cutaneous melanoma, 2 unknown). Immunohistochemical staining was performed using three primary antibodies against PD-L1 (E1L3N, SP142, and 28-8). PD-L1-positive staining in tumor cells was defined as ≥ 1% expression.

RESULTS

The positive rates were 25.0% for 28-8, 34.0% for E1L3N, and 34.0% for SP142 in 64 samples. The positive rates of acral melanoma were 10.7% for 28-8, 21.4% for E1L3N, and 21.4% for SP142. The positive rate of mucosal melanoma for which all three antibodies reacted was 12.5%. The positive rates of cutaneous melanoma were 55.6% for 28-8, 66.7% for E1L3N, and 66.7% for SP142. Significant relationships were observed among the PD-L1+ tumor cells, CD4+ TILs, and CD8+ TILs (p < 0.001).

CONCLUSION

The staining results by E1L3N, SP142, and 28-8 antibodies were within the allowable range, although the positive rates by E1L3N and P142 were slightly higher than that of 28-8. CD4+ TILs and CD8+ TILs were quantitatively correlated with PD-L1-positive tumor cells.

Concordance in judgment of clinical borders of basal cell carcinomas in Japanese patients: A preliminary study of JCOG2005 (J-BASE-MARGIN)

Basal cell carcinoma is the most common type of skin cancer, and surgical excision with clear margins is the standard of care. Surgical margins are determined based on risk factors (high or low risk) for recurrence according to the National Comprehensive Cancer Network and Japanese basal cell carcinoma guidelines. The clarity of the clinical tumor border (well-defined or poorly defined) is considered a risk factor, and significant discrepancies in the judgment of clinical tumor borders among dermato-oncologists may occur. Therefore, we analyzed the dermato-oncologists' concordance in judging the clinical tumor border of basal cell carcinoma. Forty-seven dermato-oncologists (experts: 37; young trainees: 10) participated in this study. The datasets of clinical and dermoscopic photographs of 79 Japanese cases of head and neck basal cell carcinoma were used to determine the concordance in the judgment of clinical tumor border. The probability of the border that was selected more often was used to calculate the rater agreement rate for each dataset. Correct judgment was defined as a more frequently selected border, and the concordance rate of clarity of clinical tumor border for each dermato-oncologist was calculated based on the definition of the correct judgment. A median concordance rate of 85% or higher for all dermato-oncologists was predefined as an acceptable rate for clinical use. Of the 79 datasets, rater agreement rates were 80-100%, 60-79%, and 51-59% for 55, 19, and five datasets, respectively. The median concordance rate for all dermato-oncologists was 86% (interquartile range: 82-89%). There was no significant difference in the concordance rate between the experts and the trainees (median, 87% vs. 85.5%; p = 0.58). The concordance rates of dermato-oncologists for all datasets were relatively high and acceptable for clinical use.

Usefulness of neuron-specific enolase as a serum marker of metastatic melanoma

Treatment strategies for advanced melanoma are dramatically changing, due to immune-checkpoint inhibitors and BRAF/MEK inhibitors. Nevertheless, reliable serum markers for evaluation of treatment responses and the outcome are still limited. Some previous reports suggested that serum neuron-specific enolase (sNSE) may be a useful marker for melanoma; however, its usefulness is controversial. Moreover, NSE has not been examined in vitro by using melanoma cell lines. We retrospectively evaluated sNSE and serum lactate dehydrogenase (sLDH) levels at the initial diagnosis and during therapy in 33 melanoma patients of various stages. We analyzed the NSE concentrations in cell lysates and supernatants from melanoma cell lines by enzyme-linked immunosorbent assay. The median sNSE was significantly higher in stage IV patients compared with stages I/II and III (16.3, 12.7 and 12.1 ng/mL, respectively). sNSE was elevated in 20% (2/10) of stage III and 61.1% (11/18) of stage IV patients but not in stages I/II. sNSE and sLDH tended to correspond to the total tumor volume (P = 0.48 and 0.58; 95% confidence intervals, 0.005-0172 and 0.776-0.836, respectively). The coincidence rate of sNSE and sLDH in stage IV at the initial diagnosis was 11 of 18 (61.1%). Of the remaining patients, elevated sNSE but not sLDH was observed in five patients (27.8%) and elevated sLDH but not sNSE was observed in two (11.1%). Four of the five patients showing elevated sNSE and normal sLDH were of the mucosal type. NSE was detected in both supernatant and cell lysate of all four melanoma cell lines (0.30-237.32 ng/mL and 137-483.04 ng/mg, respectively). Two cell lines with a high supernatant NSE level contained many dead cells in the supernatant. The combination of sNSE and sLDH could contribute to the early detection of distant metastasis and disease condition evaluations for advanced melanoma patients.

P4677Balloon pulmonary angioplasty improves pulmonary arterial compliance in patients with inoperable chronic thromboembolic pulmonary hypertension

Background

Right ventricular (RV) pressure overload is directly related to the increase in mortality in pulmonary hypertension. Pulmonary arterial compliance (CPA; stroke volume/pulmonary pulse pressure) was reported to be an independent determinant of RV systolic afterload in patients with pulmonary arterial hypertension (PAH). Recently, balloon pulmonary angioplasty (BPA) has been reported to reduce mean pulmonary artery pressure (mPAP) and pulmonary vascular resistance (RPA) in patients with inoperable chronic thromboembolic pulmonary hypertension (CTEPH). However, the effects of BPA on CPA remain unclear.

Purpose

The aim of this study was to investigate the impact of BPA on CPA in patients with inoperable CTEPH.

Methods

We retrospectively analyzed 78 patients (388 BPA sessions) with inoperable CTEPH who underwent BPA in our hospital from September 2012 to June 2018. Total number of BPA sessions was 5.0±1.8 (range 1–10). The pressure values were obtained from right heart catheterization at baseline (n=78), just after the final BPA (n=78) and follow-up (n=19) periods. The intervals from baseline to the final BPA and the final BPA to follow-up were 593±498 days and 397±276 days, respectively.

Results

Mean age was 60.5±12.6 years old, and 64 (82%) were female. All patients were symptomatic (WHO functional class II/III/IV 16/55/7). Patients who had pulmonary vasodilators decreased from 70 (90%) at baseline to 23 (28%) at the final BPA and 2 (15%) at follow-up. BPA reduced mPAP and RPA significantly from baseline to the final BPA and follow-up periods. BPA also improved CPA with significant reduction of pulse pressure despite no significant changes in stroke volume between baseline and follow-up (Table). CPA between the final BPA and follow-up was equivalent (p=0.95).

Conclusions

BPA improved CPA just after the final BPA in inoperable CTEPH patients. In addition, CPA was preserved during the follow-up after the final BPA sessions. These data suggest that BPA consistently unloads RV systolic afterload in those patients.

Dermoscopy of Melanoma and Non-melanoma Skin Cancers

Dermoscopy is a widely used non-invasive technique for diagnosing skin tumors. In melanocytic tumors, e.g., melanoma and basal cell carcinoma (BCC), the effectiveness of dermoscopic examination has been fully established over the past two decades. Moreover, dermoscopy has been used to diagnose non-melanocytic tumors. Here, we review novel findings from recent reports concerning dermoscopy of melanoma and non-melanoma skin cancers including BCC, sebaceous carcinoma, actinic keratosis, Bowen's disease, squamous cell carcinoma (SCC), Merkel cell carcinoma (MCC), extramammary Paget's disease (EMPD), and angiosarcoma.

Association between PD-L1 expression and lymph node metastasis in cutaneous squamous cell carcinoma

AIM

To clarify the relationship between programmed cell death ligand 1 (PD-L1) expression in cutaneous squamous cell carcinoma (cSCC) and clinicopathological variables.

METHODS

We examined PD-L1 expression in tumor cells (TCs) and tumor infiltrating immune cells (ICs) in 46 cases of cSCC by immunohistochemistry. In each case, we employed two methods-intensity and proportion scores-to evaluate PD-L1 expression in TCs. For the evaluation of PD-L1 expression in ICs, only the proportion score was used. Association between PD-L1 expression and clinicopathological variables was analyzed using Fisher's exact test.

RESULTS

High intensity scores in TCs were observed in 18 of the 46 cases (39.1%) and low intensity scores were observed in 28 cases (60.9%). Applying the proportions, using cut-off values of ≥1% and 50%, positive scores in TCs were observed in 36 (78.3%) and 20 cases (43.5%), respectively. PD-L1-positive ICs were observed in 29 (63%) and seven cases (15.2%), using cut-off values of ≥1% and 10%, respectively. The high intensity scores in TCs correlated with lymph node metastasis (P = 0.008) and female gender (P = 0.017), although positive proportions in TCs or ICs were not significantly related to lymph node metastasis. A multivariate analysis showed that high intensity of PD-L1 expression in TCs was an independent risk factor for lymph node metastasis.

CONCLUSIONS

The results suggested that high intensity of PD-L1 expression in TCs is associated with lymph node metastasis in cSCC.

Dermoscopic features distinctive for extraocular sebaceous carcinoma

We examined dermoscopic features of three cases of extraocular sebaceous carcinoma and reviewed the literatures. The yellowish structures, polymorphous vessels and ulceration were common findings in our cases and all cases of the previous reports. The appearance of whitish-pink areas has not been described previously. Our results suggested that the combination of four dermoscopic features, whitish-pink areas, yellowish structures, polymorphous vessels and ulceration might be distinctive in extraocular sebaceous carcinoma.

Successful TS-1 monotherapy as the second-line treatment for advanced extramammary Paget's disease: A report of two cases

There is no standard chemotherapeutic treatment for advanced extramammary Paget's disease, though the effectiveness of some chemotherapy regimens, including docetaxel, has been reported. In this report, we report that TS-1 monotherapy was effective in two patients with advanced extramammary Paget's disease after docetaxel treatment failure. TS-1 monotherapy may be useful as the second-line treatment for patients with advanced extramammary Paget's disease.

System for automatically inferring a genetic netwerk from expression profiles

A system is constructed to automatically infer a genetic network byapplication of graphical Gaussian modeling to the expression profiledata. Our system is composed of two parts: one part is automaticdetermination of cluster boundaries of profiles in hierarchicalclustering, and another part is inference of a genetic network byapplication of graphical Gaussian modeling to the clustered profiles.Since thousands of or tens of thousands of gene expression profiles aremeasured under only one hundred conditions, the profiles naturally showsome similar patterns. Therefore, a preprocessing for systematicallyclustering the profiles is prerequisite to infer the relationship betweenthe genes. For this purpose, a method for automatic determination ofcluster boundaries is newly developed without any biological knowledgeand any additional analyses. Then, the profiles for each cluster areanalyzed by graphical Gaussian modeling to infer the relationship betweenthe clusters. Thus, our system automatically provides a graph betweenclusters only by input the profile data. The performance of the presentsystem is validated by 2467 profiles from yeast genes. The clusters andthe genetic network obtained by our system are discussed in terms of thegene function and the known regulatory relationship between genes.

Period-phase map: two-dimensional selection of circadian rhythm-related genes

Many genes related to the circadian rhythm, especially those involved in phase shifts induced by different environmental stimuli, still remain enigmatic. In this study, the authors monitored the expression of rat genes measured with multiple phase-resetting stimuli, and developed a technique to extract the candidate genes for the changes in circadian rhythm by the stimuli, from microarray data. First, the spectra for the time series of gene expression were estimated by fast Fourier transform, and then two fitting methods, the random period fitting method and the conditional curve fitting method, using the estimated periods as the initial values, were applied to the control and the stimulated expression data to estimate the periods and the phases. Finally, by comparing the two sets of periods and phases, the period change and the phase shift by stimuli were estimated to extract the candidate genes related to the master clock, by mapping the period change and the phase shift on a two-dimensional space, a period-phase map (PPM). As an indirect validation of the genes selected by our method, the significant enrichment of extracted gene clusters on the PPM was further evaluated, in terms of biological function. As a result, the gene clusters related to photoreceptors and neural regulation emerged on the PPM, thus implying the relationships in the stimulus response of the master clock that resides in the brain at the intersection of the optic nerves. Thus, the present approach is a feasible means to explore the oscillatory genes related to stimulus responses.

Local multiple alignment of numerical sequences: detection of subtle motifs from protein sequences and structures

This paper presents a new method to find motifs from multiple protein sequences and multiple protein structures. The method consists of two parts: quantification and local multiple alignment. In the former part, protein sequences and protein structures are transformed into sequences of real numbers and real vectors respectively. In the latter part, fixed length regions having similar shapes are located. A Gibbs sampling algorithm for sequences of real numbers/vectors is newly developed for finding common regions. The results of the comparison with a standard Gibbs sampling program show that the method is particularly useful when structural information is available.

Statistical estimation of cluster boundaries in gene expression profile data

MOTIVATION

Gene expression profile data are rapidly accumulating due to advances in microarray techniques. The abundant data are analyzed by clustering procedures to extract the useful information about the genes inherent in the data. In the clustering analyses, the systematic determination of the boundaries of gene clusters, instead of by visual inspection and biological knowledge, still remains challenging.

RESULTS

We propose a statistical procedure to estimate the number of clusters in the hierarchical clustering of the expression profiles. Following the hierarchical clustering, the statistical property of the profiles at the node in the dendrogram is evaluated by a statistics-based value: the variance inflation factor in the multiple regression analysis. The evaluation leads to an automatic determination of the cluster boundaries without any additional analyses and any biological knowledge of the measured genes. The performance of the present procedure is demonstrated on the profiles of 2467 yeast genes, with very promising results.

AVAILABILITY

A set of programs will be electronically sent upon request.

CONTACT

horimoto@post.saga-med.ac.jp; toh@beri.co.jp

Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes

MOTIVATION

Following an extensive search for orthologous genes between the complete genomes from archaea and bacteria, the spatial association of the orthologs has been investigated in terms of synteny, the conservation of the order of neighboring genes. However, the relationships between the relative locations of remote orthologs over entire genomes have not been shown.

RESULTS

Comprehensive comparisons between the locations of orthologs on nineteen archaeal and bacterial genomes are presented by the location to location correspondence based on the gene-location distance. When the two genomes are rotated such that a pair of orthologs with the shortest distance is set in the same angle, a statistically significant number of orthologs maintain their relative locations between the genomes. Even by the short distances at the 5% significance level, the rotations are restricted within a narrow range, suggesting an intrinsic angle for realizing similar locations between the orthologs in each genome pair. Furthermore, the rotations in the restricted range agree with the replication origin and terminus sites for the analyzed genomes where such sites are known. The relationship between location-maintained orthologs and gene function is also discussed.

[Observation of physiological change in the human ciliary body using an ultrasound biomicroscope during accommodation]

PURPOSE

To evaluate changes in the ciliary body during accommodation using an ultrasound biomicroscope (UBM).

SUBJECTS AND METHODS

Eleven healthy persons, aged from 24 to 33 years, served as subjects. They were asked to lie in the supine position and to fixate a target placed on the ceiling 2 m above with the left eye. A concave lens with the power of -6 to -8 diopters was then placed before the fixating left eye. The thickness of the ciliary body in the right eye was measured by UBM in the nonaccommodative and accommodative states.

FINDINGS

The anterior chamber in the right eye became significantly shallow during accommodation. The thickness of the ciliary body significantly increased during accommodation at 0.5 mm and 1.0 mm posterior to the scleral spur. It significantly decreased at 2.0 mm, 2.5 mm and 3.0 mm posterior to the scleral spur.

CONCLUSION

During induced accommodation in the left eye, the anterior portion of the ciliary body in the right eye increased and the posterior portion decreased in thickness. The findings imply that the circular ciliary muscles are mainly involved in accommodation and not the longitudinal muscles.

A method for comparing circular genomes from gene locations: application to mitochondrial genomes

MOTIVATION

Data on the entire structures of organelle and bacterial genomes, most of which are known to be circular, have accumulated at a rapid pace. This information enables us to utilize the locations of homologous gene pairs for measuring the dissimilarity between complete genomic structures.

RESULTS

A macroscopic distance is presented for comparing circular genomes from their overall structures, on the basis of the locations of two pairs of homologous genes on the compared genomes. The novel aspect of our method is that the comparison between the genomes automatically reveals a relationship based on the information on all gene locations, by incorporating the mobility of each gene, which includes not only the gene order, but also the relative location between gene pairs. The plausibility of the newly defined distances is evaluated by means of 44 mitochondrial genomes. The genome distance shows high performance for quantitatively describing the differences between the gene organizations of the genomes.

AVAILABILITY

Since the programs implementing these calculations require well-arranged gene organization data, they have not been released yet. However, one of the authors will analyze circular genomes upon request. Data on the gene organizations may be submitted electronically to the address below.

Resolution of Fusarium sporotrichioides Proteins by Two-Dimensional Polyacrylamide Gel Electrophoresis and Identification by Sequence Homology Comparison in Protein Data Base

Proteins from Fusarium sporotrichioides M-1-1, a T2-toxin-producing strain, were separated by two-dimensional polyacrylamide gel electrophoresis. One thousand two hundred and forty-four protein spots were resolved and 103 protein spots were subjected to N-terminal sequencing. Fifty-eight protein spots were sequenced and 48 proteins were observed to have blocked N termini. Forty out of 58 sequenced proteins were identified by homology search against the PIR protein sequence data base and protein superfamily data base, while the residual 18 sequences were not identified. Twenty-seven of the N-terminal-blocked proteins were subjected to mild anhydrous hydrazine vapor deblocking. Twenty-four spots were not deblocked indicating the presence of acyl groups at the N termini, while 3 proteins were deblocked showing the blocked group to be pyrroglutamyl carboxylic acid residues. The results can provide a more global view of cellular genetic expression than any other technique. The created data may offer a unique opportunity to link information with DNA sequence data. Copyright 1995 S. Karger AG, Basel

Prevalence of dry eye in Japanese eye centers

BACKGROUND

The purpose of the investigation was to ascertain the prevalence of dry eye in new outpatients.

METHODS

A total of 2127 consecutive new outpatients seen in eight Japanese centers from April 1992 to January 1993 underwent comprehensive examinations, including double vital staining and measurement of tear film break-up time, basal tear secretion, and tear clearance. Dry eye was diagnosed if patients had abnormalities of both the tear film and the ocular surface.

RESULTS

Three hundred fifty-nine patients (17%) had dry eye. There was no seasonal pattern for dry eye. The condition was significantly more common in Tokyo than in suburban areas (P < 0.01). The prevalence of dry eye in visual display terminal (VDT) users and contact lens (CL) wearers was significantly higher than in non-VDT users and non-CL wearers (P < 0.05 and P < 0.02, respectively).

CONCLUSION

Our findings suggest that dry eye is one of the most common ocular disorders encountered by physicians. Furthermore, if patients use VDTs or wear CLs, the likelihood of dry eye occurring is higher.

A simple procedure for assigning a sequence motif with an obscure pattern: application to the basic/helix-loop-helix motif

We have developed a simple method to assign a sequence motif with an obscure pattern. Given a multiple sequence alignment for a region of protein that is known or strongly believed to have the same secondary and tertiary structures, the quantification method by principal component analysis is designed to find the regions most likely to have the same structure in a protein outside of the original set. The potential of this newly developed method was evaluated with reference to the known basic/helix-loop-helix (bHLH) motifs, and its characteristics were discussed with four obscure but well-defined motifs and compared with the other methods for searching sequence motifs. The method was also applied to assign the bHLH motif in Epstein-Barr virus nuclear antigen 1 (EBNA-1). This application revealed one candidate for the basic/helix 1 region and two candidates for the helix 2 region in the bHLH motif, within the region from amino acid residues 460 to 600, which is in good agreement with our previous experimental studies on the DNA binding region of EBNA-1. The basic/helix-loop-helix-loop-helix structure thus assigned suggests a function of EBNA-1 which is associated with both replication and transcription.

Ocular surface damage and tear lactoferrin in dry eye syndrome

We studied the relationship between the severity of ocular surface damage and the level of tear lactoferrin in primary and secondary Sjögren's syndrome and keratoconjunctivitis sicca not associated with Sjögren's syndrome. A significant negative correlation was found between Rose Bengal staining score and level of tear lactoferrin in all three groups. Analysis of covariance disclosed no significant differences in regression lines for Rose Bengal staining score vs tear lactoferrin level among the three groups. The three regression lines appeared to be identical to each other. These findings indicate that the severity of ocular surface damage due to dry eye largely depends on the tear secretory function of the lacrimal gland, and that the function of the lacrimal gland can be evaluated by determination of level of tear lactoferrin using the same standards regardless of differences in pathogenesis of underlying diseases.

[Evaluation of the effect of the sodium hyaluronate ophthalmic solution on tear film stability--non-contact specular microscopic evaluation]

Sodium hyaluronate solution is known to relieve various dry eye symptoms by suppressing the breakup of the preocular tear film. Using tear film stability as a parameter, we examined in 12 volunteers the time and concentration-dependent effects of sodium hyaluronate on their short precorneal tear film breakup time (BUT, 10 sec. or less) at a low tear volume (15 mm or less by using the phenol red thread test). Each subject underwent four separate study periods, receiving one of the following four ophthalmic solutions during each period: 0.05, 0.1, 0.3% w/v sodium hyaluronate (molecular weight, about 1,000,000) or the vehicle alone. BUT was measured non-invasively using a non-contact specular microscope before and 5, 15, 30, 60, 120, and 180 minutes after drug application. While BUT was not significantly prolonged after instilling either the vehicle or 0.05% solution, it was significantly increased at all times after applying either 0.1% or 0.3% solution, as compared to preinstillation. These results indicate that sodium hyaluronate solutions at concentrations of at least 0.1% can be effective in alleviating symptoms of dry eye.

Divergence pattern and selective mode in protein evolution: the example of vertebrate myoglobins and hemoglobin chains

The evolutionary relation of vertebrate myoglobin and the hemoglobin chains including the agnathan hemoglobin chain is investigated on the basis of a new view of amino acid changes that is developed by canonical discriminant analysis of amino acid residues at individual sites. In contrast to the clear discrimination of amino acid residues between myoglobin, hemoglobin alpha chain, and hemoglobin beta chain in warm-blood vertebrates, the three types of globins in the lower class of vertebrates show so much variation that they are not well discriminated. This is seen particularly at the sites that are ascertained in mammals to carry the amino acid residues participating in stabilizing the monomeric structure in myoglobin and the residues forming the subunit contacts in hemoglobin. At these sites, agnathan hemoglobin chains are evaluated to be intermediate between the myoglobin and hemoglobin chains of gnathostomes. The variation in the phylogenetically lower class of globins is also seen in the internal region; there the amino acid residues of myoglobin and hemoglobin chains in the phylogenetically higher class exhibit an example of parallel evolution at the molecular level. New quantities, the distance of sequence property between discriminated groups and the variation within each group, are derived from the values of discriminant functions along the peptide chain, and this set of quantities simply describes an overall feature of globins such that the distinction between the three types of globins has been clearer as the vertebrates have evolved to become jawed, landed, and warm-blooded. This result strongly suggests that the functional constraint on the amino acid sequence of a protein is changed by living conditions and that severe conditions constitute a driving force that creates a distinctive protein from a less-constrained protein.

Structure model of core proteins in photosystem I inferred from the comparison with those in photosystem II and bacteria; an application of principal component analysis to detect the similar regions between distantly related families of proteins

A principal component analysis based on the physico-chemical properties of amino acid residues is developed to assign similar regions between distantly related families of proteins, taking account of the species diversities in respective families. The most important advantage of this analysis should be that it reflects different physico-chemical properties and thus can predict more detailed structural properties, including the transmembrane helices, than the hydropathy analysis. Its first application reconfirms the similarity between the core proteins of photosynthetic reaction center in purple bacteria and those of photosystem II, indicating that the low percentage of identical amino acid residues estimated previously between them is due to much allowance for amino acid substitutions in purple bacteria. The application of this analysis to the core proteins of photosystem I reveals that any of these proteins includes two domains, each showing high similarity to the amino acid sequences of core proteins in photosystem II and purple bacteria. A core structure model of A1 and A2 proteins folded into four layers of sheets of transmembrane helices is proposed to provide a molecular basis for the electron pathway suggested by spectroscopic experiments as well as for the interaction sites with plastocyanin, 9 kDa protein and LHC proteins.

Principal component analysis to detect the similarity of distantly related proteins; its application to cytochromes c, c1 and f

A new method has been developed for detecting the similarity between distantly related families of proteins. The amino acid sequences of each family of proteins are vertically aligned by a homologous alignment method and the physico-chemical properties of the amino acid residues at the corresponding site are evaluated simultaneously, by method of the principal component analysis. Taking into account the species diversity of each family of proteins, we assign the similar regions between the different families of proteins by the overlapping degree of the standard deviations around the mean values of the first principal component. To investigate the homologous relationship between the electron transport proteins in photosynthetic and O2 respiratory systems, this method has been applied to 70 species of mitochondrial cytochrome c, 4 species of cytochrome c1 and 7 species of cytochrome f. This analysis reveals that both cytochrome f and cytochrome c1 have large regions which are similar to those of cytochrome c. Assuming that these similar regions have the same stereochemical structures as those in cytochrome c, we can predict the outlines of the tertiary structures of cytochrome c1 and cytochrome f, respectively, each able to interact with its electron acceptor, cytochrome c and plastocyanin.

Discrimination between adaptive and neutral amino acid substitutions in vertebrate hemoglobins

A discriminant analysis on the basis of the physicochemical properties of amino acid residues is developed to investigate the accumulation pattern of amino acid substitutions in a family of proteins. The application of this analysis to vertebrate hemoglobins reveals the following new results. (1) The major components of teleost fish and amphibian hemoglobins showing the Root effect are sharply discriminated from mammalian hemoglobins in several regions of the alpha and beta chains, whereas shark, minor components of teleost fish and amphibian, reptile, and bird hemoglobins showing no Root effect exhibit a gradual change to mammalian hemoglobin in a straightforward way. This result suggests at least two lines of molecular evolution in vertebrate hemoglobins. (2) The nonadult hemoglobin chains are allocated to the latter line, i.e., tadpole, zeta, and pi chains are similar to shark and trout I chains, and epsilon and gamma chains are similar to some of the reptile chains. (3) In any case, most of the amino acid residues causing the discrimination are located near the sites that carry the amino acid residues conserved well throughout all classes of vertebrates, suggesting that modifications adapting to the respective living conditions or respiratory organs have taken place effectively near the amino acid residues essential for the manifestation of cooperative oxygen binding. (4) The amino acid residues at other sites are changed from one to another species even within the same class, showing a constant substitution rate as a whole. These amino acid substitutions may be nearly neutral, being under a weak functional constraint. The number of sites allowing such neutral substitutions is rather small, less than one-half of all the sites in the adult hemoglobins of bird and mammal, whereas it amounts to two-thirds in teleost fish hemoglobins.

Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA

An extensive set of 216 eukaryotic 5S rRNA sequences are compared and the previous observations, that (i) invariable base positions are located primarily in loop regions and (ii) stem regions are more variable but the number of mispairings is kept small, are confirmed. On the basis of a comparison of the contemporary sequences, evolutionary processes of base substitutions in stem regions are discussed. It is found that there is no evident selective pressure to keep a particular kind of base pair in stem regions and individual bases may change freely as long as mispairings are kept few. It is also found that the secondary structure of 5S rRNA has been maintained stable by an equilibrium between base pair formation- and destruction-substitutions and that the low occurrence of mispairings in stem regions is attributable to a high value (ca. 90) of the equilibrium constant. The present analyses suggest a structure-function relationship of the eukaryotic 5S rRNA; stem regions structurally help loop regions to interact well with other ribosomal components and therefore, there is a marked selection pressure to maintain the secondary structure under the evolutionary noise of mutation.

Accumulation pattern of amino acid substitutions in protein evolution

A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This "two clock" interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.